[10-Q] Quantum-Si Incorporated Quarterly Earnings Report

Rhea-AI Filing Summary

Quantum-Si Incorporated — Condensed Q2 2025 summary

For the six months ended June 30, 2025, total revenue was $1.433 million versus $1.079 million in H1 2024, with gross profit of $0.837 million. Net loss for the six months was $48.0 million (basic and diluted loss per share $0.26); loss for the three months ended June 30, 2025 was $28.8 million (loss per share $0.16). Operating expense drivers: R&D $28.93 million and SG&A $23.78 million for H1 2025.

Balance sheet and liquidity: cash and cash equivalents $22.188 million, marketable securities $192.023 million (total liquid assets ~$214.2 million). Net cash used in operating activities for H1 2025 was $46.351 million. The Company completed a January 3, 2025 registered direct offering (gross $50.0 million; net proceeds ~$46.8 million) and management expects current liquidity to fund operations for at least 12 months from issuance date. Material items: accrued legal settlement liability $8.0 million and related insurance receivable $4.638 million recorded as of June 30, 2025; warrant liabilities fair value declined to $2.6 million from $5.0 million at year-end 2024. Accumulated deficit as of June 30, 2025 was $644.7 million.

Positive

• Raised capital: January 3, 2025 registered direct offering gross proceeds $50.0M (net ~$46.8M), improving near-term liquidity.
• Material liquid assets: cash + marketable securities total ~$214.2M, which management expects to fund operations for at least 12 months from issuance.
• Revenue growth: H1 2025 revenue of $1.433M versus H1 2024 $1.079M (increase in product and international sales).
• Warrant liability reduction: combined warrant liabilities fair value decreased to $2.6M from $5.0M at 12/31/2024, generating non-cash gains in the period.

Negative

• High operating losses and cash burn: Net loss H1 2025 $48.0M vs H1 2024 $42.6M; operating cash used $46.351M in six months.
• Large R&D and SG&A expense base: H1 2025 R&D $28.93M and SG&A $23.78M, delaying path to profitability absent substantial revenue growth.
• Legal settlement accrual: accrued legal settlement liability of $8.0M with a related insurance receivable of $4.638M; settlement is preliminary and subject to court approval.
• Accumulated deficit and dilution risk: accumulated deficit $644.7M; substantial outstanding options, RSUs and warrants (excluded from diluted EPS as anti-dilutive) pose future dilution risk.

Insights

Financial Analyst

TL;DR: Liquidity looks sufficient near term but operating cash burn and large R&D spend keep profitability distant.

The Company grew revenue modestly YoY to $1.433M for H1 2025 but remains pre-revenue scale relative to expenses: H1 net loss of $48.0M driven by $28.9M R&D and $23.8M SG&A. Cash, cash equivalents and marketable securities total ~$214.2M, and management states this plus revenue should fund operations for at least 12 months. Operating cash outflow of $46.4M in six months indicates continued high burn; the January registered direct offering provided ~$46.8M net proceeds. Warrant liabilities fell to $2.6M, providing small non-operating gains. Overall: material for investors but mixed fundamentals; monitor quarterly burn and product commercialization progress.

Corporate Governance / Risk Analyst

TL;DR: Recorded litigation accrual and indemnity exposures raise governance and contingent liability focus.

The Company recorded an $8.0M accrued legal settlement liability and a related $4.638M insurance receivable tied to the Delaware stockholder litigation, with the settlement described as preliminary and subject to court approval and execution of definitive documents. Quantum-Si previously agreed to indemnify certain Business Combination-related defendants, which may affect contingent exposures. Restructuring charges largely complete and remaining liability is immaterial. From a governance and risk perspective, the litigation settlement and indemnification framework are material contingencies that warrant continued disclosure until final approval.

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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

_____________________________________________________________

FORM 10-Q

(Mark One)

☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2025

or

o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from ________ to _________

Commission File Number: 001-39486

QUANTUM-SI INCORPORATED

(Exact name of registrant as specified in its charter)

_____________________________________________________________

Delaware						85-1388175
(State or other jurisdiction of incorporation or organization)						(I.R.S. Employer Identification No.)

29 Business Park Drive
Branford, Connecticut						06405
(Address of principal executive offices)						(Zip Code)

(866) 688-7374

(Registrant’s telephone number, including area code)

Not applicable

(Former name, former address and former fiscal year, if changed since last report)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class

Trading  Symbol(s)

Name of each exchange on which registered

Class A common stock, $0.0001 per share

QSI

The Nasdaq Stock Market LLC

Redeemable warrants, each whole warrant exercisable for one share of Class A common stock, each at an exercise price of $11.50 per share

QSIAW

The Nasdaq Stock Market LLC

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No o

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer

o

Accelerated filer

o

Non-accelerated filer

☒

Smaller reporting company

☒

Emerging growth company

o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

As of July 31, 2025, the registrant had 182,557,698 shares of Class A common stock outstanding and 19,937,500 shares of Class B common stock outstanding.

QUANTUM-SI INCORPORATED

TABLE OF CONTENTS

						Page
			Cautionary Note Regarding Forward-Looking Statements			3
Part I.			Financial Information			5
Item 1.			Financial Statements			5
			Condensed Consolidated Balance Sheets as of June 30, 2025, and December 31, 2024 (unaudited)			5
			Condensed Consolidated Statements of Operations and Comprehensive Loss for the three and six months ended June 30, 2025 and 2024 (unaudited)			6
			Condensed Consolidated Statements of Changes in Stockholders’ Equity for the three and six months ended June 30, 2025 and 2024 (unaudited)			7
			Condensed Consolidated Statements of Cash Flows for the six months ended June 30, 2025 and 2024 (unaudited)			8
			Notes to Condensed Consolidated Financial Statements (unaudited)			9
Item 2.			Management’s Discussion and Analysis of Financial Condition and Results of Operations			26
Item 3.			Quantitative and Qualitative Disclosures About Market Risk			33
Item 4.			Controls and Procedures			34
Part II.			Other Information			35
Item 1.			Legal Proceedings			35
Item 1A.			Risk Factors			35
Item 2.			Unregistered Sales of Equity Securities and Use of Proceeds			35
Item 3.			Defaults Upon Senior Securities			35
Item 4.			Mine Safety Disclosures			35
Item 5.			Other Information			35
Item 6.			Exhibits			36
Signatures						37

In this Quarterly Report on Form 10-Q, the terms “we”, “us”, “our”, the “Company” or “Quantum-Si” mean Quantum-Si Incorporated and our subsidiaries. Quantum-Si Incorporated was incorporated in Delaware on June 10, 2020.

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CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q includes forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended (the “Securities Act”), and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), that relate to future events, our future operations or financial performance, or our plans, strategies and prospects. These statements are based on the beliefs and assumptions of our management team. Although we believe that our plans, intentions and expectations reflected in or suggested by these forward-looking statements are reasonable, we cannot assure that we will achieve or realize these plans, intentions or expectations. Forward-looking statements are inherently subject to risks, uncertainties and assumptions. Generally, statements that are not historical facts, including statements concerning possible or assumed future actions, business strategies, events or performance, are forward-looking statements. The actual results may differ from its expectations, estimates, and projections and, consequently, you should not rely on these forward-looking statements as predictions of future events. Words such as “expect,” “estimate,” “project,” “budget,” “forecast,” “anticipate,” “intend,” “plan,” “may,” “will,” “could,” “should,” “believes,” “predicts,” “potential,” “continue,” and similar expressions (or the negative versions of such words or expressions) are intended to identify such forward-looking statements. These forward-looking statements include, without limitation, our expectations with respect to future performance and development and commercialization of products and services. The forward-looking statements are based on projections prepared by, and are the responsibility of, management and involve significant risks and uncertainties that could cause the actual results to differ materially from those discussed in the forward-looking statements. Most of these factors are outside our control and are difficult to predict. Forward-looking statements contained in this Quarterly Report on Form 10-Q include, but are not limited to, statements about:

•the impact of international conflicts, pandemics or epidemics on our business;

•the impact of general conditions in the global economy and in the global financial markets, including changes in inflation, interest rates, tariffs, retaliatory trade policies including limitations of shipments of products, and overall economic conditions and uncertainties;

•maintaining the listing of our Class A common stock on The Nasdaq Stock Market LLC;

•changes in applicable laws or regulations;

•our ability to raise financing in the future;

•the success, cost and timing of our product development and commercialization activities;

•the commercialization and adoption of our existing products, including our Platinum® line of instruments, our consumable kits and the success of any product we may offer in the future;

•our ability to obtain and maintain regulatory approval for our products, and any related restrictions and limitations of any approved product;

•our ability to identify, in-license or acquire additional technology;

•our ability to maintain our existing lease, license, manufacture and supply agreements;

•our ability to compete with other companies currently marketing or engaged in the development or commercialization of products and services that serve customers engaged in proteomic analysis, many of which have greater financial and marketing resources than us;

•the size and growth potential of the markets for our products and services, and our ability to serve those markets once commercialized, either alone or in partnership with others;

•our estimates regarding future expenses, future revenue, capital requirements and needs for additional financing; and

•our financial performance.

These forward-looking statements are based on information available as of the date of this report and current expectations, forecasts and assumptions, and involve a number of judgments, risks and uncertainties. Important factors could cause actual results, performance or achievements to differ materially from those indicated or implied by forward-looking statements such as those described in Part I, Item 1A, “Risk Factors” of our Annual Report on Form 10-K for the fiscal year ended December 31, 2024, in Part II, Item 1A of our Quarterly Report on Form 10-Q for the quarter ended March 31, 2025, and in other filings that we make with the Securities and Exchange Commission. The risks described under the heading “Risk Factors” are not exhaustive. New risk factors emerge from time to time, and it is not possible to predict all such risk factors, nor can we assess the impact of all such risk factors on our business or the extent to which any factor or combination of factors may cause actual results to differ materially from those contained in any forward-looking statements. Forward-looking statements are not guarantees of performance. You should not put undue reliance on these statements, which speak only as of the date hereof. All forward-looking statements attributable to us or persons acting on our behalf are expressly qualified in their entirety by the foregoing cautionary statements. We undertake no obligation to

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update or revise publicly any forward-looking statements, whether as a result of new information, future events or otherwise, except as required by law.

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PART I – FINANCIAL INFORMATION

Item 1.    Financial Statements

QUANTUM-SI INCORPORATED

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands, except share and par value amounts)

(unaudited)

			June 30, 2025						December 31, 2024
Assets
Current assets:
Cash and cash equivalents			$	22,188					$	49,241
Marketable securities			192,023						160,362
Accounts receivable, net of allowance of $140 and $124, respectively			917						1,333
Legal settlement insurance receivable			4,638						-
Inventory			3,903						4,067
Prepaid expenses and other current assets			2,805						3,006
Total current assets			226,474						218,009
Property and equipment, net			15,340						15,993
Operating lease right-of-use assets			11,782						13,061
Other assets			810						808
Total assets			$	254,406					$	247,871
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable			$	2,234					$	1,931
Accrued payroll and payroll-related costs			3,440						5,331
Accrued contracted services			2,193						2,379
Accrued legal settlement liability			8,000						—
Accrued expenses and other current liabilities			3,780						4,848
Warrant liabilities, current			2,589						—
Current portion of operating lease liabilities			1,783						3,698
Total current liabilities			24,019						18,187
Warrant liabilities, non-current			—						4,995
Operating lease liabilities			9,359						9,250
Other long-term liabilities			45						19
Total liabilities			33,423						32,451
Commitments and contingencies (Note 17)
Stockholders’ equity:
Class A Common stock, $0.0001 par value; 600,000,000 shares authorized as of June 30, 2025 and December 31, 2024; 164,357,534 and 146,953,271 shares issued and outstanding as of June 30, 2025 and December 31, 2024, respectively			16						16
Class B Common stock, $0.0001 par value; 27,000,000 shares authorized as of June 30, 2025 and December 31, 2024; 19,937,500 shares issued and outstanding as of June 30, 2025 and December 31, 2024			2						2
Additional paid-in capital			865,671						811,998
Accumulated other comprehensive (loss) income			(40)						45
Accumulated deficit			(644,666)						(596,641)
Total stockholders’ equity			220,983						215,420
Total liabilities and stockholders’ equity			$	254,406					$	247,871

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS

(in thousands, except per share amounts)

(unaudited)

			Three months ended June 30,												Six months ended June 30,
			2025						2024						2025						2024
Revenue:
Product			$	558					$	584					$	1,366					$	1,012
Service			33						38						67						67
Total revenue			591						622						1,433						1,079
Cost of revenue:
Product			230						249						567						419
Service			10						19						29						37
Total cost of revenue			240						268						596						456
Gross profit			351						354						837						623
Operating expenses:
Research and development			15,213						14,381						28,930						26,482
Selling, general and administrative			11,896						12,424						23,777						23,952
Legal settlement expense, net of insurance proceeds			3,362						—						3,362						—
Total operating expenses			30,471						26,805						56,069						50,434
Loss from operations			(30,120)						(26,451)						(55,232)						(49,811)
Dividend and interest income			2,312						2,887						4,859						6,461
Change in fair value of warrant liabilities			(994)						477						2,407						796
Other expense, net			(14)						(12)						(28)						(19)
Loss before provision for income taxes			(28,816)						(23,099)						(47,994)						(42,573)
Provision for income taxes			(20)						—						(31)						—
Net loss			$	(28,836)					$	(23,099)					$	(48,025)					$	(42,573)
Net loss per common share attributable to common stockholders, basic and diluted			$	(0.16)					$	(0.16)					$	(0.26)					$	(0.30)
Weighted-average shares used to compute net loss per share attributable to common stockholders, basic and diluted			183,625						141,939						182,968						141,856
Other comprehensive (loss) income:
Net unrealized (loss) gain on marketable securities, net of tax			$	(54)					$	28					$	(107)					$	—
Foreign currency translation adjustment			16						(2)						22						(7)
Total other comprehensive (loss) gain, net of tax			(38)						26						(85)						(7)
Comprehensive loss			$	(28,874)					$	(23,073)					$	(48,110)					$	(42,580)

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

CONDENSED CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS’ EQUITY

(in thousands, except share amounts)

(unaudited)

			Class A common stock												Class B common stock												Additional paid-in capital						Accumulated other comprehensive gain (loss)						Accumulated deficit						Total stockholders’ equity
			Shares						Amount						Shares						Amount
Balance - December 31, 2024			146,953,271						$	16					19,937,500						$	2					$	811,998					$	45					$	(596,641)					$	215,420
Common stock issued upon exercise of stock options			623,834						—						—						—						1,600						—						—						1,600
Common stock issued upon vesting of restricted stock units			358,511						—						—						—						—						—						—						—
Common stock issued from direct equity offering, net of fees and issuance costs			15,625,000						—						—						—						46,774						—						—						46,774
Stock-based compensation			—						—						—						—						2,362						—						—						2,362
Net unrealized loss on marketable securities, net of tax			—						—						—						—						—						(53)						—						(53)
Foreign currency translation			—						—						—						—						—						6						—						6
Net loss			—						—						—						—						—						—						(19,189)						(19,189)
Balance - March 31, 2025			163,560,616						$	16					19,937,500						$	2					$	862,734					$	(2)					$	(615,830)					$	246,920
Common stock issued upon exercise of stock options			24,583						—						—						—						41						—						—						41
Common stock issued upon vesting of restricted stock units			772,335						—						—						—						—						—						—						—
Stock-based compensation			—						—						—						—						2,896						—						—						2,896
Net unrealized loss on marketable securities, net of tax			—						—						—						—						—						(54)						—						(54)
Foreign currency translation			—						—						—						—						—						16						—						16
Net loss			—						—						—						—						—						—						(28,836)						(28,836)
Balance - June 30, 2025			164,357,534						$	16					19,937,500						$	2					$	865,671					$	(40)					$	(644,666)					$	220,983

			Class A common stock												Class B common stock												Additional paid-in capital						Accumulated other comprehensive (loss) gain						Accumulated deficit						Total stockholders’ equity
			Shares						Amount						Shares						Amount
Balance - December 31, 2023			121,832,417						$	12					19,937,500						$	2					$	767,239					$	—					$	(495,634)					$	271,619
Common stock issued upon vesting of restricted stock units			46,572						—						—						—						—						—						—						—
Stock-based compensation			—						—						—						—						1,645						—						—						1,645
Net unrealized loss on marketable securities, net of tax			—						—						—						—						—						(28)						—						(28)
Refund of issuance costs			—						—						—						—						14						—						—						14
Foreign currency translation			—						—						—						—						—						(5)						—						(5)
Net loss			—						—						—						—						—						—						(19,474)						(19,474)
Balance - March 31, 2024			121,878,989						$	12					19,937,500						$	2					$	768,898					$	(33)					$	(515,108)					$	253,771
Common stock issued upon exercise of stock options			96,069						—						—						—						136						—						—						136
Common stock issued upon vesting of restricted stock units			407,274						—						—						—						—						—						—						—
Stock-based compensation			—						—						—						—						2,426						—						—						2,426
Net unrealized gain on marketable securities, net of tax			—						—						—						—						—						28						—						28
Foreign currency translation			—						—						—						—						—						(2)						—						(2)
Net loss			—						—						—						—						—						—						(23,099)						(23,099)
Balance - June 30, 2024			122,382,332						$	12					19,937,500						$	2					$	771,460					$	(7)					$	(538,207)					$	233,260

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

(unaudited)

			Six Months Ended June 30,
			2025						2024
Cash flows from operating activities:
Net loss			$	(48,025)					$	(42,573)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization			2,108						2,448
Non-cash lease expense			1,279						1,190
Accretion on marketable securities			(4,263)						(4,323)
Loss on disposal of fixed assets			15						—
Write-down of inventory			997						1,567
Change in fair value of warrant liabilities			(2,407)						(796)
Stock-based compensation			5,258						4,071
Other			—						22
Changes in operating assets and liabilities:
Accounts receivable, net			416						(230)
Legal settlement insurance receivable			(4,638)						—
Inventory			(766)						(1,748)
Prepaid expenses and other current assets			186						886
Accounts payable			46						(105)
Accrued expenses and other current liabilities			(2,777)						(518)
Accrued legal settlement liability			8,000						—
Other long-term liabilities			26						(1,656)
Operating lease liabilities			(1,806)						4
Net cash used in operating activities			(46,351)						(41,761)
Cash flows from investing activities:
Purchases of property and equipment			(1,634)						(2,173)
Internally developed software - capitalized costs			—						(59)
Purchases of marketable securities			(191,605)						(208,788)
Sales and maturities of marketable securities			164,100						178,400
Net cash used in investing activities			(29,139)						(32,620)
Cash flows from financing activities:
Proceeds from exercise of stock options			1,641						136
Proceeds from issuance of common stock from direct equity offering, net of fees and issuance costs			46,774						—
Deferred offering costs			—						(70)
Refund of issuance costs			—						14
Net cash provided by financing activities			48,415						80
Effect of exchange rate changes on cash and cash equivalents			22						(7)
Net decrease in cash and cash equivalents			(27,053)						(74,308)
Cash and cash equivalents at beginning of period			49,241						133,860
Cash and cash equivalents at end of period			$	22,188					$	59,552
Supplemental disclosure of cash flow information:
Cash paid for income taxes			$	—					$	108
Supplemental disclosure of non-cash investing and financing activities:
Property and equipment purchased but not paid			$	440					$	280
Deferred offering costs payable			$	—					$	75

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Note 1. Description of Business and Basis of Presentation

Background

Quantum-Si Incorporated (including its subsidiaries, the “Company” or “Quantum-Si”) was incorporated in Delaware on June 10, 2020 as HighCape Capital Acquisition Corp. (“HighCape”). The Company’s legal name became Quantum-Si Incorporated following a business combination on June 10, 2021 between the Company and Q-SI Operations Inc. (formerly Quantum-Si Incorporated) (the “Business Combination”), which was founded in 2013.

Quantum-Si is a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. The Company has developed a proprietary universal single-molecule detection platform that it is applying to proteomics to enable Next-Gen Protein SequencingTM (“NGPS”), to sequence proteins in a massively parallel fashion (rather than sequentially, one at a time), which can also be used for the study of nucleic acids. The Company believes that the ability to sequence proteins in a massively parallel fashion and offer a fast analysis time provides NGPS with the potential to unlock significant biological information through improved resolution and unbiased access to the proteome at a speed and scale that is not available today. Traditionally, proteomic workflows to sequence proteins required days or weeks to complete. The Company’s platform includes its Platinum line of NGPS instruments, Platinum Analysis Software, and consumable kits for use with its Platinum line of instruments.

Liquidity and Capital Resources

The Company has historically financed its operations primarily with proceeds from the issuance of equity to private investors, as well as with the proceeds received from the closing of the Business Combination. The Company has incurred significant losses and negative cash flows from operations in all periods since inception and had an accumulated deficit of $644.7 million as of June 30, 2025. The Company has incurred significant operating losses, including net losses of $48.0 million and $42.6 million for the six months ended June 30, 2025 and 2024, respectively. As of June 30, 2025, the Company had cash, cash equivalents and investments in marketable securities of $214.2 million. Management believes that the Company’s current cash, cash equivalents and marketable securities, together with revenue from the sales of its products and services, will be sufficient to fund its planned operations for at least the next twelve months from the date of the issuance of the accompanying Condensed Consolidated Financial Statements.

Until such time as the Company can generate significant revenue from product sales, if ever, it expects to finance its operations through private and public equity offerings, debt financings, and/or potential future collaboration, license and development agreements. However, there can be no assurance that the Company will be able to complete any such transactions on acceptable terms or otherwise, and the Company may be unable to obtain sufficient additional capital when needed. The inability to raise capital as and when needed would have a negative impact on the Company’s financial condition and its ability to pursue its business strategy. The Company will need to generate significant revenue to achieve profitability and it may never do so.

Global Developments

Although the U.S. Federal Reserve lowered interest rates slightly in 2024, it is not known whether additional action will be taken to lower interest rates and if this decrease, and any other decreases, will have an impact on inflation. While these rate fluctuations have not had a significant adverse impact on the Company to date, the impact of such rate increases on the overall financial markets and the economy may adversely impact the Company in the future. In addition, the global economy has experienced and is continuing to experience high levels of inflation and global supply chain disruptions. The Company continues to monitor these supply chain, inflation and interest rate factors, as well as the uncertainty resulting from the overall economic environment.

To date, the Company has not been materially affected by enacted tariffs either by the U.S. government or foreign retaliatory tariffs, however, the Company’s finished goods and/or their components could become materially affected by changing tariffs in the future. If increased tariffs are imposed on the Company’s finished goods and/or components, they may impact the business, financial condition, results of operations and cash flows.

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Although the Company has not been significantly impacted by geopolitical conflicts throughout the world, the Company has experienced some constraints in product and material availability and increasing costs required to obtain some materials and supplies as a result of these conflicts on the global economy. To date, the business has not been materially impacted by these conflicts, however, as the conflicts continue or worsen, it may impact the business, financial condition, results of operations and cash flows.

Basis of Presentation and Principles of Consolidation

The accompanying Condensed Consolidated Financial Statements include the accounts of the Company and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and pursuant to the accounting disclosure rules and regulations of the Securities and Exchange Commission (the “SEC”). All intercompany transactions are eliminated.

These Condensed Consolidated Financial Statements should be read in conjunction with the audited Consolidated Financial Statements and the notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024. The Condensed Consolidated Balance Sheet as of December 31, 2024 included herein was derived from the audited Consolidated Financial Statements as of that date, but does not include all disclosures, including certain notes required by U.S. GAAP, on an annual reporting basis.

In the opinion of management, the accompanying Condensed Consolidated Financial Statements reflect all normal recurring adjustments necessary to fairly state the financial position, results of operations, and cash flows for the interim periods. The results for the three and six months ended June 30, 2025 are not necessarily indicative of the results to be expected for any subsequent quarter, the year ending December 31, 2025, or any other period.

There have been no material changes to the Company’s significant accounting policies as described in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024.

Reclassifications

Certain prior year amounts have been reclassified for consistency with the current year’s presentation.

Note 2. Summary of Significant Accounting Policies

For the Company’s Significant Accounting Policies, please refer to its Annual Report on Form 10-K for the fiscal year ended December 31, 2024. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the Accounting Standards Codification and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”).

Use of Estimates

The preparation of the Condensed Consolidated Financial Statements in conformity with U.S. GAAP requires the Company to make estimates and assumptions about future events that may affect the amounts recorded in its Condensed Consolidated Financial Statements and accompanying notes. Future events and their effects cannot be determined with certainty. On an ongoing basis, management evaluates these estimates and assumptions. Significant estimates and assumptions include:

•inventory valuation;

•assumptions used for leases;

•valuation of warrant liabilities;

•valuation allowances with respect to deferred tax assets;

•assumptions associated with revenue recognition; and

•assumptions underlying the fair value used in the calculation of stock-based compensation.

The Company bases these estimates on historical and anticipated results and trends and on various other assumptions the Company believes are reasonable under the circumstances, including assumptions as to future events. Changes in estimates are recorded in the period in which they become known. Actual results could differ from those estimates, and any such differences may be material to the Condensed Consolidated Financial Statements.

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Recently Issued Accounting Pronouncements

In May 2025, the FASB issued ASU 2025-04, Compensation-Stock Compensation (Topic 718) and Revenue from Contracts with Customers (Topic 606): Clarifications to Share-Based Consideration Payable to a Customer. This standard aims to reduce diversity in practice and improve the decision usefulness and operability of the guidance for share-based consideration payable to a customer in conjunction with selling goods or services. The ASU is effective for fiscal years beginning after December 15, 2026 with early adoption permitted. The ASU is to be applied on a retrospective or modified retrospective basis. The Company is currently evaluating the impact ASU 2025-04 may have on its Consolidated Financial Statements and disclosures.

In May 2025, the FASB issued ASU 2025-03, Business Combinations (Topic 805) and Consolidation (Topic 810): Determining the Accounting Acquirer in the Acquisition of a Variable Interest Entity. This standard clarifies the guidance in determining the acquirer in an acquisition transaction effected primarily by exchanging equity interests when the legal acquiree is a VIE that meets the definition of a business. The amendments require that an entity consider the same factors that are currently required for determining which entity is the accounting acquirer in other acquisition transactions. This guidance is effective for fiscal years beginning after December 15, 2026 with early adoption permitted. The ASU is required to be applied prospectively to any acquisition transaction that occurs after the initial application date. ASU 2025-03 does not currently have an impact on the Consolidated Financial Statements and disclosures however, the Company will continue to monitor for any future impact ASU 2025-03 may have on its Consolidated Financial Statements and disclosures.

In November 2024, the FASB issued ASU No. 2024-03, Disaggregation of Income Statement Expenses (“DISE”), which requires additional disclosure of the nature of expenses included in the income statement. The ASU requires disclosures about specific types of expenses included in the expense captions presented on the face of the income statement as well as disclosures about selling expenses. The amendments in this update are effective for annual reporting periods beginning after December 15, 2026 and interim reporting periods beginning after December 15, 2027, with early adoption permitted. The ASU is required to be applied prospectively with the option for retrospective application. The Company is currently evaluating the impact ASU 2024-03 may have on its Consolidated Financial Statements and disclosures.

In March 2024, the FASB issued ASU No. 2024-02, Codification Improvements - Amendments to Remove References to the Concepts Statements, which contains amendments to the Codification that remove references to various Concepts Statements. The amendments in ASU 2024-02 are not intended to result in significant accounting changes for most entities. The Company adopted ASU 2024-02 effective January 1, 2025. The adoption of ASU 2024-02 did not have a material impact to the Consolidated Financial Statements and disclosures.

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures, which expands income tax disclosure requirements to include additional information related to the rate reconciliation of effective tax rates to statutory rates, as well as additional disaggregation of taxes paid in both U.S. and foreign jurisdictions. The amendments in ASU 2023-09 also remove disclosures related to certain unrecognized tax benefits and deferred taxes. The amendments are effective for fiscal years beginning after December 31, 2024, with early adoption permitted. The new standard is expected to apply prospectively, but retrospective application is permitted. The Company will adopt the new standard for the year ended December 31, 2025 and is currently evaluating the impact ASU 2023-09 may have on its Consolidated Financial Statements and disclosures.

Note 3. Investments in Marketable Securities

As of June 30, 2025 and December 31, 2024, the Company’s investments in marketable securities were determined to be available-for-sale securities.

Dividend and interest income from marketable securities related to the Company’s available-for-sale securities for the three and six months ended June 30, 2025 were as follows (in thousands):

			Three months ended June 30,												Six months ended June 30,
			2025						2024						2025						2024
Dividend income from marketable securities			$	155					$	368					$	376					$	1,343
Interest income from marketable securities			$	2,157					$	2,519					$	4,483					$	5,118

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The following is a summary of the Company’s available-for-sale securities recorded within Marketable securities on the Condensed Consolidated Balance Sheets as of June 30, 2025 and December 31, 2024 (in thousands):

			June 30, 2025
			Amortized Costs						Gross Realized Net Losses						Gross Unrealized Net Losses						Fair Value
Financial Assets:
Short-term marketable securities:
U.S. Treasury securities			$	87,518					$	—					$	(6)					$	87,512
Commercial paper			104,543						—						(32)						104,511
Total			$	192,061					$	—					$	(38)					$	192,023

			December 31, 2024
			Amortized Costs						Gross Realized Net Gains						Gross Unrealized Net Gains						Fair Value
Financial Assets:
Short-term marketable securities:
U.S. Treasury securities			$	108,047					$	—					$	63					$	108,110
Commercial paper			52,243						—						9						52,252
Total			$	160,290					$	—					$	72					$	160,362

The fair values of the Company’s available-for-sale securities included within Marketable securities on the Condensed Consolidated Balance Sheets as of June 30, 2025 and December 31, 2024, by remaining contractual maturity, are as follows (in thousands):

			June 30, 2025
			One Year or Less						Over One Year Through Five Years						Over Five Years						Total
Financial Assets:
Short-term marketable securities:
U.S. Treasury securities			$	87,512					$	—					$	—					$	87,512
Commercial paper			104,511						—						—						104,511
Total			$	192,023					$	—					$	—					$	192,023

			December 31, 2024
			One Year or Less						Over One Year Through Five Years						Over Five Years						Total
Financial Assets:
Short-term marketable securities:
U.S. Treasury securities			$	108,110					$	—					$	—					$	108,110
Commercial paper			52,252						—						—						52,252
Total			$	160,362					$	—					$	—					$	160,362

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Note 4. Fair Value of Financial Instruments

Fair value estimates of financial instruments are made at a specific point in time, based on relevant information about financial markets and specific financial instruments. As these estimates are subjective in nature, involving uncertainties and matters of significant judgment, they cannot be determined with precision. Changes in assumptions can significantly affect estimated fair value.

The Company measures fair value as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The Company utilizes a three-tier hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value:

•Level 1: Valuations based on quoted prices in active markets for identical assets or liabilities that an entity has the ability to access.

•Level 2: Valuations based on quoted prices for similar assets or liabilities, quoted prices for identical assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable data for substantially the full term of the assets or liabilities.

•Level 3: Valuations based on inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

The carrying value of cash and cash equivalents, accounts payable and accrued expenses and other current liabilities approximates their fair values due to the short-term or on demand nature of these instruments. As of June 30, 2025 and December 31, 2024, the Company’s investment portfolio included available-for-sale securities which were comprised of money market funds, U.S. Treasury bills and commercial paper. The Company has U.S. Treasury bills and commercial papers that are classified as Level 2 due to the fair value for these instruments being determined by utilizing observable inputs in similar assets or identical assets in non-active markets. The fair value of certain of the U.S. Treasury bills transferred to Level 2 from Level 1 of the fair value hierarchy due to trading activity, observability and accessibility of the pricing information from the most active market of the investment.

Warrants are recorded as Warrant liabilities, current and Warrant liabilities on the Condensed Consolidated Balance Sheets as of June 30, 2025 and December 31, 2024, respectively. The warrant liabilities are measured at fair value at inception and on a recurring basis, with changes in fair value presented as Change in fair value of warrant liabilities in the Condensed Consolidated Statements of Operations and Comprehensive Loss.

The Public Warrants and Private Warrants were carried at fair value as of June 30, 2025 and December 31, 2024. The Public Warrants were valued using Level 1 inputs as they are traded in an active market. The Private Warrants were valued using a binomial lattice model. The primary unobservable input utilized in determining the fair value of the Private Warrants was the expected volatility of the Company’s Class A common stock. The expected volatility was based on consideration of the implied volatility from the Company’s own Public Warrant pricing and on the historical volatility observed at guideline public companies. As of June 30, 2025, the significant assumptions used in preparing the binomial lattice model for valuing the Private Warrants liability include (i) volatility of 202.7%, (ii) risk-free interest rate of 4.0%, (iii) strike price of $11.50, (iv) fair value of Class A common stock of $1.96, and (v) expected life of 0.9 years. As of December 31, 2024, the significant assumptions used in preparing the binomial lattice model for valuing the Private Warrants liability include (i) volatility of 194.3%, (ii) risk-free interest rate of 4.2%, (iii) strike price of $11.50, (iv) fair value of Class A common stock of $2.70, and (v) expected life of 1.4 years.

There were no exercises or redemptions of the Public Warrants or Private Warrants during the three and six months ended June 30, 2025 and 2024.

The following table summarizes the Company’s assets and liabilities on the Condensed Consolidated Balance Sheets as of June 30, 2025 and December 31, 2024, that are measured at fair value on a recurring basis, by level, within the fair value hierarchy (in thousands):

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						June 30, 2025
						Level 1						Level 2						Level 3						Total
Financial Assets:
Cash equivalents:
Money market funds						$	20,224					$	—					$	—					$	20,224
Commercial paper						—						—						—						—
Marketable securities:
U.S. Treasury securities						—						87,512						—						87,512
Commercial paper						—						104,511						—						104,511
Total assets at fair value on a recurring basis						$	20,224					$	192,023					$	—					$	212,247
Liabilities:
Public Warrants						$	2,492					$	—					$	—					$	2,492
Private Warrants						—						—						97						97
Total liabilities at fair value on a recurring basis						$	2,492					$	—					$	97					$	2,589

						December 31, 2024
						Level 1						Level 2						Level 3						Total
Financial Assets:
Cash equivalents:
Money market funds						$	20,340					$	—					$	—					$	20,340
U.S. Treasury securities						16,919						—						—						16,919
Marketable securities:
U.S. Treasury securities						—						108,110						—						108,110
Commercial paper						—						52,252						—						52,252
Total assets at fair value on a recurring basis						$	37,259					$	160,362					$	—					$	197,621
Liabilities:
Public Warrants						$	4,792					$	—					$	—					$	4,792
Private Warrants						—						—						203						203
Total liabilities at fair value on a recurring basis						$	4,792					$	—					$	203					$	4,995

Note 5. Inventory

Inventory consists of the following as of June 30, 2025 and December 31, 2024 (in thousands):

			June 30, 2025						December 31, 2024
Raw materials			$	1,036					$	1,290
Work in progress			2,009						2,212
Finished goods			858						565
Total inventory			$	3,903					$	4,067

Charges recorded for inventory write-downs included in Research and development expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss were $0.2 million and $1.0 million for the three months ended June 30, 2025 and 2024, respectively, and $0.7 million and $1.6 million for the six months ended June 30, 2025 and 2024, respectively.

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Charges recorded for inventory write-downs included in Cost of revenue in the Condensed Consolidated Statements of Operations and Comprehensive Loss were $0.1 million and immaterial for the three months ended June 30, 2025 and 2024, respectively, and $0.3 million and $0.1 million for the six months ended June 30, 2025 and 2024, respectively.

Note 6. Property and Equipment, Net

Property and equipment, net, consists of the following as of June 30, 2025 and December 31, 2024 (in thousands):

			June 30, 2025						December 31, 2024
Laboratory and production equipment			$	14,149					$	13,412
Computer equipment			1,693						1,724
Purchased software			57						57
Furniture and fixtures			318						321
Leasehold improvements			11,635						7,226
Construction in process			1,565						4,960
Subtotal			29,417						27,700
Less: Accumulated depreciation and amortization			(14,077)						(11,707)
Property and equipment, net			$	15,340					$	15,993

Depreciation and amortization expense is included within Cost of revenue, Research and development and Selling, general and administrative expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Depreciation and amortization expense was $1.2 million and $1.4 million for the three months ended June 30, 2025 and 2024, respectively, and $2.1 million and $2.4 million for the six months ended June 30, 2025 and 2024, respectively. No impairments were recorded for the three and six months ended June 30, 2025 and 2024.

Note 7. Leases

Lease-related costs for the three and six months ended June 30, 2025 and 2024 are as follows (in thousands):

			Three months ended June 30,												Six months ended June 30,
			2025						2024						2025						2024
Operating lease cost			$	864					$	864					$	1,728					$	1,728
Variable lease cost			439						392						823						828
Total lease cost			$	1,303					$	1,256					$	2,551					$	2,556

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Future minimum lease payments under non-cancellable leases as of June 30, 2025 are as follows (dollars in thousands):

			Remaining Lease Payments
Remainder of 2025			$	2,272
2026			4,585
2027			4,549
2028			2,975
2029			2,806
Thereafter			7,247
Total remaining undiscounted lease payments			$	24,434
Less: Imputed interest			(4,188)
Less: Lease incentives(1)			(9,104)
Total lease liabilities			11,142
Less: current portion			(1,783)
Long-term operating lease liabilities			$	9,359
Weighted-average remaining lease term (in years)			5.1
Weighted-average discount rate			7.9		%

(1)Includes lease incentives estimated to be realized in 2026 and 2027 for the costs of leasehold improvements.

The following table provides certain cash flow and supplemental cash flow information related to the Company’s lease liabilities for the six months ended June 30, 2025 and 2024 (in thousands):

			Six months ended June 30,
			2025						2024
Operating cash paid to settle operating lease liabilities			$	2,254					$	2,196

As of both June 30, 2025 and December 31, 2024, the Company incurred and recognized total leasehold improvements of approximately $1.2 million related to reimbursable construction costs which are included in construction in progress within Property and equipment, net, on the Condensed Consolidated Balance Sheets.

Note 8. Accrued Expenses and Other Current Liabilities

As of June 30, 2025 and December 31, 2024, Accrued expenses and other current liabilities included on the Condensed Consolidated Balance Sheets consist of the following (in thousands):

			June 30, 2025						December 31, 2024
Legal fees			$	1,592					$	2,166
Sales tax payable			1,378						1,339
Restructuring costs			289						679
Deferred revenue			99						189
Royalties			156						150
Other			266						325
Total accrued expenses and other current liabilities			$	3,780					$	4,848

Note 9. Equity Transactions

Registered Direct Offering

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On January 3, 2025, the Company entered into a securities purchase agreement with certain institutional investors pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “January 2025 Registered Direct Offering”) an aggregate of 15,625,000 shares of the Company’s Class A common stock at a price of $3.20 per share. The gross proceeds to the Company from the January 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds recorded as of June 30, 2025 were approximately $46.8 million.

Preferred Stock

As of June 30, 2025 and December 31, 2024, the Company had authorized 1,000,000 shares of preferred stock at $0.0001 par value per share. There were no preferred shares outstanding for both periods.

Preferred stock may be issued from time to time in one or more series. Any shares of preferred stock which may be redeemed, purchased or acquired by the Company may be reissued except as otherwise provided by law.

Note 10. Stock-based Compensation

Equity Incentive Plan

The Quantum-Si Incorporated 2021 Equity Incentive Plan (the “2021 Plan”) provides for grants of stock options, stock appreciation rights, restricted stock, restricted stock units, and other stock or cash-based awards. Directors, officers and other employees of the Company and its subsidiaries, as well as others performing consulting or advisory services for the Company, are eligible for grants under the 2021 Plan. As of June 30, 2025, there were 13,134,075 shares available for future grant under the 2021 Plan.

Inducement Equity Incentive Plan

On May 8, 2023, the Company adopted the 2023 Inducement Equity Incentive Plan (the “2023 Inducement Plan”) to reserve 3,000,000 shares of its Class A common stock to be used exclusively for grants of awards to individuals that were not previously employees or directors of the Company as a material inducement to such individuals’ entry into employment with the Company within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. On August 23, 2024, the Company amended the 2023 Inducement Plan to reserve an additional 3,000,000 shares of its Class A common stock under the 2023 Inducement Plan. The terms and conditions of the 2023 Inducement Plan, as amended, are substantially similar to those of the 2021 Plan. As of June 30, 2025, there were 1,562,494 shares available for future issuance under the 2023 Inducement Plan, as amended.

Stock Options

The Company granted participants an aggregate of 1,134,855 and 1,166,855 stock option awards during the three and six months ended June 30, 2025, respectively, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates. During both the three and six months ended June 30, 2024, the Company granted an aggregate of 1,547,306 stock option awards to participants with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

The Company recorded $1.7 million and $1.8 million for stock-based compensation related to stock options for the three months ended June 30, 2025 and 2024, respectively, and $3.2 million and $3.1 million for stock-based compensation related to stock options for the six months ended June 30, 2025 and 2024, respectively.

The fair value of each stock option award granted during the six months ended June 30, 2025 was estimated as of the grant date using a Black-Scholes model with the following assumptions:

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						Six months ended June 30, 2025
Expected term (in years)						4.6 - 5.5
Risk-free interest rate						4.4%
Expected volatility						107.4% - 114.0%
Expected dividend yield						—
Weighted average grant date fair value per share						$1.15 - $1.88

A summary of the stock option activity for the six months ended June 30, 2025 is presented in the table below:

			Number of Options						Weighted Average Exercise Price (per share)						Weighted Average Remaining Contractual Term (in years)						Aggregate Intrinsic Value (in thousands)
Outstanding at December 31, 2024			20,803,142						$	2.61					7.8						$	11,507
Granted			1,166,855						1.44
Exercised			(648,417)						2.53
Forfeited			(630,135)						3.75
Outstanding at June 30, 2025			20,691,445						$	2.51					7.5						$	3,669
Options exercisable at June 30, 2025			10,305,351						$	3.03					6.7						$	1,100
Vested and expected to vest at June 30, 2025			18,307,712						$	2.58					7.5						$	3,079

As of June 30, 2025, total unrecognized stock-based compensation related to stock options was $9.5 million, which is expected to be recognized over a remaining weighted average vesting period of 1.9 years.

Performance Stock Options

In November 2022 and May 2023, the Company granted 2,780,000 and 1,000,000 performance-based stock option awards to its Chief Executive Officer and Chief Financial Officer, respectively. The vesting of these awards are subject to continued service to the Company and certain market conditions. The market conditions require the Company’s Class A common stock trade above specified levels for certain periods of time. The fair values of the awards were estimated at the grant date using the Monte Carlo simulation model.

On March 15, 2024, the market conditions that trigger the vesting of these performance-based stock option awards were modified. The modified market conditions require the Company’s Class A common stock to trade above specified levels for certain defined periods of time that are different from the original awards. The Company accounted for the modifications as modifications of market conditions. The total incremental stock-based compensation expense to be recognized for these awards within Selling, general and administrative operating expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss is approximately $2.4 million. Incremental stock-based compensation expense was $0.2 million and $0.4 million for the three and six months ended June 30, 2025, respectively and $0.2 million for both the three and six months ended June 30, 2024.

Restricted Stock Units

The Company granted participants an aggregate of 77,270 and 8,181,743 restricted stock unit (“RSU”) awards during the three and six months ended June 30, 2025, respectively, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates. During the three and six months ended June 30, 2024, the Company granted an aggregate of 923,209 and 6,329,373 RSU awards to participants with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

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The Company recorded $1.3 million and $0.7 million for stock-based compensation related to RSU awards for the three months ended June 30, 2025 and 2024, respectively, and $2.1 million and $1.0 million for stock-based compensation related to RSU awards for the six months ended June 30, 2025 and 2024, respectively.

A summary of the RSU activity for the six months ended June 30, 2025 is presented in the table below:

			Number of Shares Underlying RSUs						Weighted Average Grant-Date Fair Value
Outstanding non-vested RSUs at December 31, 2024			7,179,009						$	1.39
Granted			8,181,743						1.21
Vested			(1,130,846)						1.57
Forfeited			(393,945)						1.26
Outstanding non-vested RSUs at June 30, 2025			13,835,961						1.28

As of June 30, 2025, total unrecognized stock-based compensation related to restricted stock units was $16.7 million, which is expected to be recognized over the remaining weighted average vesting period of 3.3 years.

Stock-based compensation is allocated to Research and development and Selling, general and administrative operating expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Stock-based compensation expense for the three and six months ended June 30, 2025 and 2024 was allocated as follows (in thousands):

			Three months ended June 30,												Six months ended June 30,
			2025						2024						2025						2024
Research and development			$	810					$	768					$	1,406					$	1,258
Selling, general and administrative			2,086						1,658						3,852						2,813
Total stock-based compensation			$	2,896					$	2,426					$	5,258					$	4,071

Note 11. Warrant Liabilities

Public Warrants

As of June 30, 2025 and December 31, 2024, there were an aggregate of 3,833,319 outstanding Public Warrants, which entitle the holder to acquire Class A common stock. Each whole warrant entitles the registered holder to purchase one share of Class A common stock at an exercise price of $11.50 per share, subject to adjustment as discussed below, beginning on September 9, 2021. The warrants will expire on June 10, 2026 or earlier upon redemption or liquidation.

Redemptions

At any time while the warrants are exercisable, the Company may redeem not less than all of the outstanding Public Warrants:

• in whole and not in part;

•at a price of $0.01 per warrant;

•upon not less than 30 days’ prior written notice of redemption (the “30-day redemption period”) to each warrant holder; and

•if, and only if, the closing price of the Company’s Class A common stock equals or exceeds $18.00 per share (as adjusted for stock splits, stock capitalizations, reorganizations, recapitalizations and the like) for any 20 trading days within a 30-trading day period ending three business days before the Company sends the notice of redemption to the warrant holders.

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If the foregoing conditions are satisfied and the Company issues a notice of redemption of the Public Warrants at $0.01 per warrant, each holder of Public Warrants will be entitled to exercise their Public Warrants held prior to the scheduled redemption date.

If the Company calls the Public Warrants for redemption for $0.01 as described above, the Board may elect to require any holder that wishes to exercise his, her or its Public Warrants to do so on a “cashless basis.” If the Board makes such election, all holders of Public Warrants would pay the exercise price by surrendering their warrants for that number of shares of Class A common stock equal to the quotient obtained by dividing (x) the product of the number of shares of Class A common stock underlying the warrants, multiplied by the excess of the “fair market value” over the exercise price of the warrants by (y) the “fair market value”. For purposes of the redemption provisions of the warrants, the “fair market value” means the average last reported sale price of the Class A common stock for the 10 trading days ending on the third trading day prior to the date on which the notice of redemption is sent to the holders of warrants.

The Public Warrants do not meet the criteria to be classified in stockholders’ equity as the exercise of the Public Warrants may be settled in cash upon the occurrence of a tender offer or exchange offer in which the maker of the tender offer or exchange offer, upon completion of the tender offer or exchange offer, beneficially owns more than 50% of the outstanding shares of the Company’s Class A common stock, even if it would not result in a change of control of the Company. This provision precludes the Public Warrants from being classified in equity and thus they are classified as current and long-term liabilities on the Condensed Consolidated Balance Sheets as of June 30, 2025 and December 31, 2024, respectively.

Private Warrants

As of June 30, 2025 and December 31, 2024, there were 135,000 Private Warrants outstanding. The Private Warrants are identical to the Public Warrants, except that so long as they are held by HighCape Capital Acquisition LLC or any of its permitted transferees, (i) the Private Warrants and the shares of Class A common stock issuable upon the exercise of the Private Warrants were not transferable, assignable or saleable until 30 days after the completion of the Business Combination, (ii) the Private Warrants will be exercisable for cash or on a cashless basis, at the holder’s option, and (iii) the Private Warrants are not subject to the Company’s redemption option at the price of $0.01 per warrant. The Private Warrants are subject to the Company’s redemption option at the price of $0.01 per warrant, provided that the other conditions of such redemption are met, as described above. If the Private Warrants are held by a holder other than HighCape Capital Acquisition LLC or any of its permitted transferees, the Private Warrants will be redeemable by the Company in all redemption scenarios applicable to the Public Warrants and exercisable by such holders on the same basis as the Public Warrants.

The Private Warrants do not meet the criteria to be classified in stockholders’ equity as the terms of the warrants provide for potential changes to the settlement amounts depending upon the characteristics of the warrant holder, and, because the holder of a warrant is not an input into the pricing of a fixed-for-fixed option on equity shares. This provision precludes the Private Warrants from being classified in equity and thus they are classified as current and long-term liabilities on the Condensed Consolidated Balance Sheets as of June 30, 2025 and December 31, 2024, respectively.

As of June 30, 2025 and December 31, 2024, the combined fair value of warrant liabilities was $2.6 million and $5.0 million, respectively. The Company recognized a loss of $1.0 million and a gain of $0.5 million as a Change in fair value of warrant liabilities in the Condensed Consolidated Statements of Operations and Comprehensive Loss for the three months ended June 30, 2025 and 2024, respectively. The Company recognized gains of $2.4 million and $0.8 million as a Change in fair value of warrant liabilities in the Condensed Consolidated Statements of Operations and Comprehensive Loss for the six months ended June 30, 2025 and 2024, respectively. There were no exercises or redemptions of the Public Warrants or Private Warrants during the three and six months ended June 30, 2025 or 2024.

For further details regarding the warrant liabilities, please refer to Note 4. Fair Value of Financial Instruments.

Note 12. Net Loss Per Share

The Company presents both basic earnings per share (“EPS”) and diluted EPS. Basic and diluted net loss per share was the same for each period presented as the inclusion of all common share equivalents would have been anti-dilutive.

The following table presents the calculations for the three and six months ended June 30, 2025 and 2024 of basic and diluted net loss per share for the Company’s common stock (in thousands, except per share amounts):

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			Three months ended June 30,												Six months ended June 30,
			2025						2024						2025						2024
Numerator
Net loss			$	(28,836)					$	(23,099)					$	(48,025)					$	(42,573)
Numerator for basic and diluted EPS - loss attributable to common stockholders			$	(28,836)					$	(23,099)					$	(48,025)					$	(42,573)
Denominator
Common stock			183,625						141,939						182,968						141,856
Denominator for basic and diluted EPS - weighted-average common stock			183,625						141,939						182,968						141,856
Basic and diluted net loss per share			$	(0.16)					$	(0.16)					$	(0.26)					$	(0.30)

Net loss per share attributable to Class A and Class B common stockholders was the same on a basic and diluted basis, as the inclusion of all potential common equivalent shares outstanding would have been anti-dilutive. The following potential dilutive shares were excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive for both the three and six months ended June 30, 2025 and 2024 (in thousands):

			Six months ended June 30, 2025
			2025						2024
Outstanding options to purchase common stock			20,691,445						22,987,156
Outstanding restricted stock units			13,835,961						6,369,699
Outstanding warrants			3,968,319						3,968,319
			38,495,725						33,325,174

Note 13. Restructuring

The Company committed to organizational restructurings during the fourth quarter of 2024, designed to decrease its costs and create a more streamlined organization to support its business. The Company expects total restructuring charges to be approximately $2.4 million. Restructuring liabilities were $0.3 million and $0.7 million as of June 30, 2025 and December 31, 2024, respectively. These liabilities are included in Accrued expenses and other current liabilities on the Condensed Consolidated Balance Sheets.

The Company’s restructuring costs, primarily for cash severance and other severance costs, are allocated to the following operating expense categories as follows (in thousands):

						Research and development						Selling, general and administrative						Total
Balance as of December 31, 2024						$	513					$	166					$	679
Restructuring charges incurred(1)						134						—						134
Cash payments and other adjustments(1)						(346)						(142)						(488)
Balance as of March 31, 2025						301						24						325
Restructuring charges incurred(1)						178						—						178
Cash payments and other adjustments(1)						(190)						(24)						(214)
Balance as of June 30, 2025						$	289					$	—					$	289
Current liabilities																		$	289
Long-term liabilities																		—
Total liabilities as of June 30, 2025																		$	289

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(1) Restructuring charges incurred and Cash payments and other adjustments include non-cash charges related to stock-based compensation expense and charges for cash severance and other severance costs, including health care coverage for a specified period of time after separation.

The Company’s restructuring activities were complete as of December 31, 2024. The Company does not expect to incur material additional charges associated with these activities.

Note 14. Income Taxes

Income taxes for the three and six months ended June 30, 2025 and 2024 were recorded at the Company’s estimated annual effective income tax rate, subject to adjustments for discrete events, if they occur. The Company’s estimated annual effective tax rate for the three and six months ended June 30, 2025 was (0.11)% and (0.06)%, respectively. The Company’s estimated annual effective tax rate for each of the three and six months ended June 30, 2024 was 0.0%. The primary reconciling items between the federal statutory rate of 21.0% and the Company’s overall effective tax rate of 0.0% for these periods were related to stock-based compensation, the valuation allowance recorded against the full amount of the Company’s net deferred tax assets and cash taxes of our cost-plus foreign subsidiary.

A valuation allowance is required when it is more likely than not that some portion or all of the Company’s deferred tax assets will not be realized. The realization of deferred tax assets depends on the generation of sufficient future taxable income during the period in which the Company’s related temporary differences become deductible. Management believes that based on the earnings history of the Company, it is more likely than not that the benefits of these assets will not be realized, and therefore, a full valuation allowance has been recorded against the Company’s net deferred tax assets as of June 30, 2025 and December 31, 2024.

On July 4, 2025, subsequent to the close of the second quarter of 2025, the One Big Beautiful Bill Act (“OBBBA”) was enacted in the United States. The OBBBA includes changes to U.S. tax and related laws. The legislation has multiple effective dates, with certain provisions effective in 2025 and other provisions implemented through 2027. The Company is currently assessing the impact on the Consolidated Financials Statements.

Note 15. Segment Information

Quantum-Si is a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. Our platform includes our Platinum NGPS instrument, Platinum Analysis Software, and consumable kits for use with our Platinum line of instruments.

The Company’s Chief Operating Decision Maker (the “CODM”), its Chief Executive Officer, reviews financial information presented on a consolidated basis for purposes of assessing financial performance, making operating decisions and allocating resources. Accordingly, the Company has determined that it operates as a single reportable segment. The CODM utilizes the Company’s long-range plan, which includes product development roadmaps and long-range financial models, as a key input to resource allocation. The CODM makes decisions on resource allocation, assesses the performance of the business, and monitors budget versus actual results on a consolidated basis using loss from operations as reported on the Condensed Consolidated Statements of Operations and Comprehensive Loss. Net loss and the change in cash and cash equivalents and marketable securities are also measures that are considered in monitoring budget versus actual results.

Significant expenses within loss from operations, as well as within net loss, include research and development, and selling, general and administrative expenses, which are each separately presented on the Company’s Condensed Consolidated Statements of Operations and Comprehensive Loss.

The Company’s revenue is derived from sales of products and services. Product revenue is primarily generated from the sales of instruments and consumables used in protein sequencing and analysis. Service revenue is primarily generated from service maintenance contracts including access to analysis software and advanced training for instrument use.

Total revenue generated from domestic and international sales for the three and six months ended June 30, 2025 and 2024 is as follows (in thousands):

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						Three months ended June 30,												Six months ended June 30,
						2025						2024						2025						2024
Domestic						$	156					$	180					$	279					$	417
International						435						442						1,154						662
Total revenue						$	591					$	622					$	1,433					$	1,079

Note 16. Related Party Transactions

The Company was a party to the Amended and Restated Technology Services Agreement (the “ARTSA”), most recently amended on November 11, 2020, by and among 4Catalyzer Corporation (“4C”), the Company and other participant companies controlled by Dr. Jonathan Rothberg, the Chairman of the Company’s Board of Directors. The Company entered into a First Addendum to the ARTSA on February 17, 2021 pursuant to which the Company agreed to terminate its participation under the ARTSA no later than immediately prior to the effective time of the Business Combination, resulting in the termination of the Company’s participation under the ARTSA on June 10, 2021. In connection with the termination of the Company’s participation under the ARTSA, the Company terminated its existing arm’s length lease agreement with 4C and negotiated an arm’s length lease agreement. Under the ARTSA, the Company and the other participant companies had agreed to share certain non-core technologies, which means any technologies, information or equipment owned or otherwise controlled by the participant company that are not specifically related to the core business area of the participant and subject to certain restrictions on use. The ARTSA also provided for 4C to perform certain services for the Company and each other participant company such as monthly administrative, management and technical consulting services to the Company which were pre-funded approximately once per quarter.

The Company incurred immaterial expenses paid to 4C for the three months ended June 30, 2025 and $0.1 million for the three months ended June 30, 2024. Expenses paid to 4C were $0.1 million for both the six months ended June 30, 2025 and 2024. These expenses included amounts for month-to-month sublease arrangements for office and laboratory spaces from 4C and certain administrative expenses. These amounts are included in Selling, general and administrative expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss. As of both June 30, 2025 and December 31, 2024 amounts due to 4C for these arrangements were immaterial.

The ARTSA also provided for the participant companies to provide other services to each other. As of June 30, 2025, amounts payable to or from the Company related to these services were immaterial. There were no such amounts payable to or from the Company as of December 31, 2024.

Effective November 1, 2022, the Company entered into an Advisory Agreement with Dr. Rothberg (the “Advisory Agreement”), pursuant to which Dr. Rothberg previously served as Chairman of the Board, advises the Chief Executive Officer and the Board on strategic matters, and provides consulting, business development and similar services on matters relating to the Company’s current, future and potential scientific and strategic initiatives and such other consulting services reasonably requested from time to time. Pursuant to the Advisory Agreement, as compensation for the services provided, in March 2023, the Company granted Dr. Rothberg an option to purchase 250,000 shares of Class A common stock pursuant to the 2021 Plan. In connection with the Advisory Agreement, Dr. Rothberg’s title was changed from Executive Chairman to Chairman of the Board. Subsequently, in May 2024, with Charles Kummeth’s appointment as Chairman of the Board, Dr. Rothberg’s title was changed from Chairman of the Board to Director.

Note 17. Commitments and Contingencies

Commitments

Licenses related to certain intellectual property:

The Company licenses certain intellectual property, some of which may be utilized in its current or future product offerings. To preserve the right to use such intellectual property, the Company is required to make annual minimum fixed payments totaling approximately $0.2 million as well as royalties based on net sales if the royalties exceed annual minimum fixed payments. As of both June 30, 2025 and December 31, 2024, the Company had accrued royalties of approximately $0.2 million included in Accrued expenses and other current liabilities on the Condensed Consolidated Balance Sheets.

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Other commitments:

The Company sponsors a 401(k) defined contribution plan covering all eligible U.S. employees (the “401(k) Plan”). Contributions to the 401(k) Plan are discretionary. The Company did not make any matching contributions to the 401(k) Plan for the three and six months ended June 30, 2025 and 2024.

Contingencies

The Company is subject to claims in the ordinary course of business. Except as discussed below, the Company is not currently a party to any pending or threatened litigation, the outcome of which would be expected to have a material adverse effect on its financial condition, results of operations, or cash flows. The Company discloses contingent liabilities even if the liability is not probable or estimable, or both, if there is a reasonable possibility that a material loss may have been incurred.

On May 16, 2024, a punitive class action lawsuit was filed in the Delaware Court of Chancery, styled Farzad v. HighCape Capital, et al. (the “Delaware Stockholder Litigation”). The Delaware Stockholder Litigation asserts breach of fiduciary duty claims against the former officers and directors of HighCape, including Kevin Rakin, Matt Zuga, David Colpman, Robert Taub and Antony Loebel, HighCape Capital Acquisition LLC and HighCape Capital L.P., aiding and abetting breach of fiduciary duty claims against Foresite Capital Management, LLC and Dr. Rothberg, and unjust enrichment claims against all defendants related to the Business Combination. The Delaware Stockholder Litigation complaint alleges that the transactions contemplated by the Business Combination were a product of an unfair process which was allegedly impacted by conflicts of interest, resulting in mispricing of the Business Combination. Quantum-Si, as part of the Business Combination, had previously agreed to indemnify certain of the defendants related to actions such as the Delaware Stockholder Litigation to the extent allowable by law.

On July 22, 2025, the parties of the Delaware Stockholder Litigation, through a mediation process, reached a preliminary settlement. As a result, as of June 30, 2025, the Company recorded a gross Accrued legal settlement liability of $8.0 million and a $4.6 million Legal settlement insurance receivable in the Condensed Consolidated Balance Sheets and associated legal settlement fees of $3.4 million in Legal settlement, net of insurance proceeds, in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Of the $8.0 million accrued liability, $7.6 million represents the preliminary legal settlement amount and $0.4 million is an estimate of legal and related expenses to finalize the legal settlement.

The preliminary legal settlement is subject to execution of definitive documentation and a number of court procedural processes, including notice to and approval of the class members, and final court approval. These activities are estimated to take 4-6 months to complete. The Company deemed these remaining court procedural processes as probable of occurring.

In April 2023, the Company informed the contract manufacturer that had manufactured the Platinum and another development product, Carbon™, that it intended to wind down the relationship and transition to a different contract manufacturer. In October 2023, the former contract manufacturer filed a complaint against the Company in the State of Texas alleging breach of contract and made claims for economic damage and attorney costs. In January 2024, the suit was withdrawn and refiled in the State of Minnesota alleging similar claims. The Company denied all liability and countersued alleging claims of negligence. In July 2025, a non-binding settlement conference took place and discussions between the parties are on-going. Although it is not possible to determine the potential financial exposure associated with the alleged claim at the time of this filing, the Company continues to believe it has a meritorious defense and intends to vigorously defend against all claims asserted in the complaint. The Company has determined the outcome of this matter is not estimable or probable.

In December 2021, the Company signed a 10-year lease for approximately 67,000 square feet of space in New Haven, Connecticut. The lease commenced on January 8, 2022 with rent payments beginning on July 7, 2022. Under the lease, the landlord contractually agreed to reimburse the Company for up to $9.1 million in improvements to the space, to be used for such improvements as the Company deems “necessary or desirable”. On September 13, 2022, the Company filed a lawsuit against the landlord, alleging that the landlord has: (i) refused to reimburse the Company for costs related to improvements already incurred and submitted, (ii) delayed the Company’s completion of improvements, in order to avoid reimbursing the costs of those improvements, and (iii) improperly rejected the Company’s proposed improvement plans. The Company accounted for these lease incentives as an offset to the lease liability recorded at the inception of the lease. In September 2024, the Company determined there was a change in the estimated timing of receipt of reimbursements for the improvements. This resulted in an increase of the carrying value of the right-of-use asset and the corresponding lease

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liabilities of $1.0 million. Although the Company believes it is contractually entitled to the $9.1 million of lease incentives, based on the current status of the litigation, the Company cannot determine the likely outcome or estimate the impact on such carrying values.

The Company enters into agreements that contain indemnification provisions with other parties in the ordinary course of business, including business partners, investors, contractors, and the Company’s officers, directors and certain employees. The Company has agreed to indemnify and defend the indemnified party claims and related losses suffered or incurred by the indemnified party from actual or threatened third-party claims because of the Company’s activities or non-compliance with certain representations and warranties made by the Company. It is not possible to determine the maximum potential loss under these indemnification provisions due to the Company’s limited history of prior indemnification claims and the unique facts and circumstances involved in any particular case. To date, losses recorded in the Condensed Consolidated Statements of Operations and Comprehensive Loss in connection with the indemnification provisions have not been material.

Note 18. Subsequent Event

On July 3, 2025, the Company entered into a securities purchase agreement with a certain institutional investor pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “July 2025 Registered Direct Offering”), an aggregate of (i) 18,200,000 shares of the Company’s Class A common stock at a price of $1.67 per share and (ii) pre-funded warrants to purchase 11,740,119 shares of common stock (the “Pre-Funded Warrants”). Each of the Pre-Funded Warrants is exercisable for one share of Class A common stock at the exercise price of $0.0001 per Pre-Funded Warrant. The Pre-Funded Warrants are immediately exercisable and may be exercised at any time until all of the Pre-Funded Warrants issued in the July 2025 Registered Direct Offering are exercised in full. The gross proceeds to the Company from the July 2025 Registered Direct Offering were approximately $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds were approximately $46.9 million. The July 2025 Registered Direct Offering closed on July 8, 2025.

In connection with the July 2025 Registered Direct Offering, the Company entered into a placement agency agreement with A.G.P./Alliance Global Partners (the “Placement Agent”), pursuant to which the Placement Agent agreed to serve as the sole placement agent for the Company, on a reasonable best efforts basis. The Company agreed to pay the Placement Agent an aggregate cash fee equal to 6.0% of the gross proceeds received in the July 2025 Registered Direct Offering.

In addition, in connection with the July 2025 Registered Direct Offering, the Company provided written notice, effective as of July 3, 2025, to Canaccord Genuity LLC of its election to terminate the equity distribution agreement dated December 11, 2024 for the Company’s at-the-market offering. At the time of termination, the Company had sold 23,425,650 shares of its Class A common stock under the equity distribution agreement for aggregate gross proceeds of $36.2 million.

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Item 2.    Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis provides information which management believes is relevant to an assessment and understanding of our condensed consolidated results of operations and financial condition. The discussion should be read in conjunction with (i) the unaudited Condensed Consolidated Financial Statements and notes thereto contained in this Quarterly Report on Form 10-Q, (ii) the Consolidated Financial Statements and notes thereto for the year ended December 31, 2024 contained in our Annual Report on Form 10-K for the year ended December 31, 2024, filed with the Securities and Exchange Commission (the “SEC”) on March 3, 2025, and (iii) our other public reports filed with the SEC. This discussion contains forward looking statements and involves numerous risks and uncertainties, including, but not limited to, those described in the “Risk Factors” section of our Annual Report on Form 10-K for the year ended December 31, 2024, and our Quarterly Report on Form 10-Q for the quarter ended March 31, 2025, and in other filings that we make with the Securities and Exchange Commission. Actual results may differ materially from those contained in any forward-looking statements. Unless the context otherwise requires, references to “we”, “us”, “our”, the “Company” or “Quantum-Si” are intended to mean the business and operations of Quantum-Si Incorporated and its consolidated subsidiaries. The unaudited Condensed Consolidated Financial Statements for the three and six months ended June 30, 2025 and 2024 present the financial position and results of operations of Quantum-Si Incorporated and its consolidated subsidiaries.

Overview

We are a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. We have developed a proprietary universal single-molecule detection platform that we are applying to proteomics to enable Next-Gen Protein SequencingTM (“NGPS”), to sequence proteins in a massively parallel fashion (rather than sequentially, one at a time), which can also be used for the study of nucleic acids. We believe that the ability to sequence proteins in a massively parallel fashion and offer a fast analysis time provides NGPS with the potential to unlock significant biological information through improved resolution and unbiased access to the proteome at a speed and scale that is not available today. Traditionally, proteomic workflows to sequence proteins required days or weeks to complete. Our platform includes our Platinum NGPS instrument, Platinum Analysis Software, and consumable kits for use with our Platinum line of instruments. In 2021, we introduced our Platinum early access program to sites with participation from leading academic centers and key industry partners. The early access program introduced the Platinum single-molecule sequencing system to key opinion leaders across the globe for both expansion and development of applications and workflows. We began a controlled launch of the Platinum instrument and started to take orders in December 2022, and subsequently began a controlled commercial launch of Platinum in January 2023, and then moved to a full commercial launch of Platinum beginning the second quarter of 2024. In January 2025, we announced the launch of our Platinum Pro benchtop sequencer. First shipments of Platinum Pro occurred in March 2025.

Going forward, we intend to follow a systematic, phased approach to continue to successfully launch updates and enhancements to our platform which can include improvements to our hardware, software and chemistry that works together to produce the overall platform.

We believe that our platform offers a differentiated solution in a rapidly evolving proteomics tools market. Within our initial focus market of proteomics, our platform is designed to provide users a seamless opportunity to gain key insights into the immediate state of biological pathways and cell state. Our platform aims to address many of the key challenges and bottlenecks with legacy proteomic solutions, such as mass spectrometry (“MS”), which include high instrument costs both in terms of acquisition and ownership, and complexity with data analysis, which together limit broad adoption. We believe our platform, which is designed to streamline sequencing and data analysis at a lower instrument cost and with greater automation than legacy proteomic solutions, could allow our product to have wide utility across the study of the proteome. For example, our platform could be used for biomarker discovery and disease detection, pathway analysis, immune response, vaccine development, quality assurance and quality control, among other applications.

Our evolving product roadmap provides for continued updates and enhancements to our current platform including instrumentation, consumable kits and software tools. We intend to execute on this roadmap through a combination of internal development programs and external partnerships to bring to market the most comprehensive proteomics platform in our industry. For example, in November 2024 we announced our next generation platform, ProteusTM, which is estimated to launch in the second half of 2026.

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Proteus aims to provide single molecule, amino acid level resolution while also providing significantly higher sequencing output per sample, increased sample throughout per run, automation of the sequencing workflow and automated data analysis. The Proteus platform is being developed to be a modular, scalable system that allows for expansion in the overall platform, the number of consumables that be processed concurrently and the overall output of sample data from the platform. The first generation of Proteus and associated sequencing consumables is anticipated to include motion control, liquid handling, and a new on-board single optical system with the ability to accept a new consumable chip that has approximately 80 million features. We believe this new platform will provide much deeper insights while simplifying and significantly reducing the cost of the underlying consumable.

Results of Operations for the Three and Six Months Ended June 30, 2025 as Compared to the Three and Six Months Ended June 30, 2024

The following table presents the Condensed Consolidated Statements of Operations and Comprehensive Loss for the three and six months ended June 30, 2025 and 2024 (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Revenue:
Product			$	558					$	584					$	(26)					(4.5)		%				$	1,366					$	1,012					$	354					35.0		%
Service			33						38						(5)						(13.2)		%				67						67						—						—		%
Total revenue			591						622						(31)						(5.0)		%				1,433						1,079						354						32.8		%
Cost of revenue:
Product			230						249						(19)						(7.6)		%				567						419						148						35.3		%
Service			10						19						(9)						(47.4)		%				29						37						(8)						(21.6)		%
Total cost of revenue			240						268						(28)						(10.4)		%				596						456						140						30.7		%
Gross profit			351						354						(3)						(0.8)		%				837						623						214						34.3		%
Operating expenses:
Research and development			15,213						14,381						832						5.8		%				28,930						26,482						2,448						9.2		%
Selling, general and administrative			11,896						12,424						(528)						(4.2)		%				23,777						23,952						(175)						(0.7)		%
Legal settlement expense, net of insurance proceeds			3,362						—						3,362						nm(1)						3,362						—						3,362						nm(1)
Total operating expenses			30,471						26,805						3,666						13.7		%				56,069						50,434						5,635						11.2		%
Loss from operations			(30,120)						(26,451)						(3,669)						13.9		%				(55,232)						(49,811)						(5,421)						10.9		%
Dividend and interest income			2,312						2,887						(575)						(19.9)		%				4,859						6,461						(1,602)						(24.8)		%
Change in fair value of warrant liabilities			(994)						477						(1,471)						(308.4)		%				2,407						796						1,611						202.4		%
Other expense, net			(14)						(12)						(2)						16.7		%				(28)						(19)						(9)						47.4		%
Loss before provision for income taxes			(28,816)						(23,099)						(5,717)						24.7		%				(47,994)						(42,573)						(5,421)						12.7		%
Provision for income taxes			(20)						—						(20)						nm(1)						(31)						—						(31)						nm(1)
Net loss			$	(28,836)					$	(23,099)					$	(5,737)					24.8		%				$	(48,025)					$	(42,573)					$	(5,452)					12.8		%

(1) “nm” indicates change is not meaningful.

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Revenue, Cost of Revenue and Gross Profit

Revenue is derived from sales of products and services. Product revenue is generated from the following sources: (i) sales of our Platinum line of instruments, (ii) consumables kits, including library preparation kits, sequencing kit (which includes sequencing reagents and semiconductor chips), and other related reagent kits, and (iii) freight revenue, which is recognized upon shipment. Service revenue is generated from service maintenance contracts including Platinum Analysis Software access, and advanced training for instrument use.

Cost of revenue primarily consists of product and service costs including material costs, personnel costs and benefits, inbound and outbound freight, packaging, warranty replacement costs, royalty costs, facilities costs, depreciation and amortization expense, and inventory write-offs.

Revenue, Cost of revenue and Gross profit for the three and six months ended June 30, 2025 and 2024 are as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Revenue:
Product			$	558					$	584					$	(26)					(4.5)		%				$	1,366					$	1,012					$	354					35.0		%
Service			33						38						(5)						(13.2)		%				67						67						—						—		%
Total revenue			591						622						(31)						(5.0)		%				1,433						1,079						354						32.8		%
Cost of revenue:
Product			230						249						(19)						(7.6)		%				567						419						148						35.3		%
Service			10						19						(9)						(47.4)		%				29						37						(8)						(21.6)		%
Total cost of revenue			240						268						(28)						(10.4)		%				596						456						140						30.7		%
Gross profit			$	351					$	354					$	(3)					(0.8)		%				$	837					$	623					$	214					34.3		%
Gross profit margin			59.4		%				56.9		%																58.4		%				57.7		%

Total revenue for the sale of our Platinum line of instruments, related reagent kits and service maintenance contracts decreased by $31 thousand, or 5.0% for the three months ended June 30, 2025 when compared to the same period in 2024, and increased $0.4 million, or 32.8%, for the six months ended June 30, 2025 when compared to the same period in 2024. For the three months ended June 30, 2025, the Company experienced longer capital sales cycles, largely driven by low or no capital spend budgets at certain customers, primarily from actual and potential budget cuts from the National Institute of Health (“NIH”). For the six months ended June 30, 2025, revenue was higher, but primarily from the contribution of the first quarter 2025 results, which largely occurred before significant NIH funding constraints were announced, as well as general higher momentum in our commercialization efforts year over year in the first quarter.

Total cost of revenue decreased $28 thousand, or 10.4%, and increased $0.1 million, or 30.7% for the three and six months ended June 30, 2025, respectively, as compared to the same periods in 2024. The change in the cost of revenue is based on the relative volume and revenue decrease for the three months ended June 30, 2025 as compared to the prior year and increase in volume and revenue for the six months ended June 30, 2025 compared to the prior year.

Gross profit was flat for the three months ended June 30, 2025 and increased $0.2 million, or 34.3%, for the six months ended June 30, 2025 as compared to the same periods in 2024.

Gross profit margin was 59.4% and 58.4% for the three and six months ended June 30, 2025, respectively, as compared to 56.9% and 57.7% for the same periods in 2024, respectively. This change in margin was primarily based on the mix of products sold during each period and includes approximately a 13% and 7% benefit for the three and six months ended June 30, 2025 and approximately a 9% and 11% benefit for the three and six months ended June 30, 2024, respectively, for inventory utilized that was carried at low or no value that predates the commercial launch of our Platinum line of instruments. Our gross profit margin will continue to be impacted by this utilized inventory and has also been impacted and

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may continue to be impacted by inventory acquisition costs. We expect gross profit margin to be variable for the foreseeable future as we work through our continued commercialization efforts.

We began a controlled launch of the Platinum instrument and started to take orders in December 2022, and subsequently began a controlled commercial launch of Platinum in January 2023, and then moved to a full commercial launch of Platinum beginning in the second quarter of 2024. In January 2025, we announced the launch of our Platinum Pro benchtop sequencer. First shipments of Platinum Pro occurred in March 2025.

Research and Development Expenses

Research and development expenses primarily consist of personnel costs and benefits, stock-based compensation, lab supplies, consulting and professional services, fabrication services, charges related to product without an alternative future use, facilities costs, software, and other outsourced expenses. Research and development expenses are recognized as incurred. Our research and development expenses are primarily related to developing new products and services.

Research and development expenses for the three and six months ended June 30, 2025 and 2024 are as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Research and development			$	15,213					$	14,381					$	832					5.8		%				$	28,930					$	26,482					$	2,448					9.2		%

Research and development expenses increased by $0.8 million, or 5.8%, for the three months ended June 30, 2025, when compared to the same period in 2024. This increase was primarily driven by a $2.0 million increase in fabrication and outsourced services partially offset by a $0.5 million decrease in payroll and payroll-related costs, a $0.4 million decrease in write-downs of inventory that no longer had an alternative future use and a $0.2 million decrease in professional services and consulting fees.

Research and development expenses increased by $2.4 million, or 9.2%, for the six months ended June 30, 2025, when compared to the same period in 2024. This increase was primarily due to a $3.8 million increase in fabrication and outsourced services partially offset by a $0.8 million decrease in payroll and payroll-related costs and a $0.4 million decrease in write-downs of inventory that no longer had an alternative future use.

In general, our research and development expenses have increased as we continue development on our Proteus platform announced in November 2024.

Selling, General and Administrative Expenses

Selling, general and administrative expenses primarily consist of personnel costs and benefits, stock-based compensation, patent and filing fees, consulting and professional services, legal and accounting services, facilities costs, depreciation and amortization expense, insurance and office expenses, product advertising and marketing.

Selling, general and administrative expenses for the three and six months ended June 30, 2025 and 2024 are as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Selling, general and administrative			$	11,896					$	12,424					$	(528)					(4.2)		%				$	23,777					$	23,952					$	(175)					(0.7)		%

Selling, general and administrative expenses decreased $0.5 million, or 4.2%, for the three months ended June 30, 2025, when compared to the same period in 2024. This decrease was primarily due to a $0.2 million decrease in tax expense, a $0.2 million decrease in depreciation expense, a $0.2 million decrease in payroll and payroll-related costs, a $0.1 million decrease in software expense, a $0.1 million decrease in legal fees and a $0.2 million net decrease in other expenses. These decreases were partially offset by a $0.4 million increase in stock-based compensation and a $0.1 million increase in professional services and consulting fees.

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Selling, general and administrative expenses decreased $0.2 million, or 0.7%, for the six months ended June 30, 2025, when compared to the same period in 2024. This decrease was primarily due to $0.4 million decrease in depreciation expense, a $0.3 million decrease in legal fees, a $0.2 million decrease in insurance costs, a $0.2 million decrease in software expense, a $0.1 million decrease in tax expense and a $0.4 million net decrease in other expenses. These decreases were partially offset by a $1.0 million increase in stock-based compensation expense and a $0.3 million increase in payroll-and payroll-related costs.

Legal Settlement Expense, Net of Proceeds

For the three and six months ended June 30, 2025 and 2024, Legal settlement expense, net of proceeds is as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Legal settlement expense, net of insurance proceeds			$	3,362					$	—					$	3,362					nm(1)						$	3,362					$	—					$	3,362					nm(1)

Legal settlement expense, net of insurance proceeds increased $3.4 million for the three and six months ended June 30, 2025, as compared to the same periods in 2024. This increase was due to a preliminary legal settlement being reached for the Delaware Stockholder Litigation. For further information on the Delaware Stockholder Litigation, please refer to Note 17. Commitments and Contingencies, in the notes to the Condensed Consolidated Financial Statements.

Dividend and Interest Income

For the three and six months ended June 30, 2025 and 2024, dividend and interest income is derived primarily from fixed income securities and money market mutual funds.

Dividend and interest income for the three and six months ended June 30, 2025 and 2024 is as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Dividend and interest income			$	2,312					$	2,887					$	(575)					(19.9)		%				$	4,859					$	6,461					$	(1,602)					(24.8)		%

Dividend and interest income decreased by $0.6 million and $1.6 million for the three and six months ended June 30, 2025, respectively, as compared to the same respective periods in 2024. These decreases are a result of lower market interest rates on invested capital and lower average invested capital in the three and six months ended June 30, 2025.

Change in Fair Value of Warrant Liabilities

Warrant liabilities were recorded at fair value as part of the Business Combination. Change in fair value of warrant liabilities primarily consists of the change in the fair value of our Public Warrants and Private Warrants.

Change in warrant liabilities for the three and six months ended June 30, 2025 and 2024 is as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Change in fair value of warrant liabilities			$	(994)					$	477					$	(1,471)					(308.4)		%				$	2,407					$	796					$	1,611					202.4		%

For the three months ended June 30, 2025, we recognized $1.0 million of expense from the increase in the fair value of warrant liabilities as compared to $0.5 million of income from the decrease in the fair value of warrant liabilities for the same period in 2024, resulting in an increase in expense of $1.5 million, or 308.4%.

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For the six months ended June 30, 2025, we recognized $2.4 million of income from the decrease in the fair value of warrant liabilities as compared to $0.8 million of income from the decrease in the fair value of warrant liabilities for the same period in 2024, an increase in income of $1.6 million, or 202.4%.

These changes in the fair value of warrant liabilities were primarily driven by the change in the underlying trading price of our Class A common stock during the periods reported.

Other Expense, Net

Other expense, net, typically consists of currency revaluations and income from credit card cash rewards programs. Other expense, net, for the three and six months ended June 30, 2025 and 2024 is as follows (dollars in thousands):

			Three months ended June 30,																								Six months ended June 30,
			2025						2024						$ Change						% Change						2025						2024						$ Change						% Change
Other expense, net			$	(14)					$	(12)					$	(2)					16.7		%				$	(28)					$	(19)					$	(9)					47.4		%

Other expense, net, increased slightly for both the three and six months ended June 30, 2025 as compared to the same periods in 2024.

Liquidity and Capital Resources

The following table presents a summary of our consolidated cash flows for operating, investing, and financing activities for the six months ended June 30, 2025 and 2024 (in thousands):

			Six months ended June 30,
			2025						2024
Net cash used in operating activities			$	(46,351)					$	(41,761)
Net cash used in investing activities			(29,139)						(32,620)
Net cash provided by financing activities			48,415						80
Effect of exchange rate changes on cash and cash equivalents			22						(7)
Net decrease in cash and cash equivalents			$	(27,053)					$	(74,308)

Net cash used in operating activities

For the six months ended June 30, 2025, net cash used in operating activities of $46.4 million was primarily due to a net loss of $48.0 million resulting from continued spend on research and development and commercialization efforts, accretion on marketable securities of $4.3 million, a change in fair value of warrant liabilities of $2.4 million, primarily driven by the change in the underlying trading price of our Class A common stock, and net changes in operating assets and liabilities of $1.3 million partially offset by stock-based compensation of $5.3 million, depreciation and amortization of $2.1 million, non-cash lease expense of $1.3 million and write-downs of inventory of $1.0 million.

For the six months ended June 30, 2024, net cash used in operating activities of $41.8 million was primarily due to a net loss of $42.6 million resulting from continued spend on research and development and commercialization efforts, accretion on marketable securities of $4.3 million, net changes in operating assets and liabilities of $3.4 million, and a change in fair value of warrant liabilities of $0.8 million, primarily driven by the change in the underlying trading price of our Class A common stock partially offset by stock-based compensation of $4.1 million, depreciation and amortization of $2.4 million, write-downs of inventory of $1.6 million and non-cash lease expense of $1.2 million.

Net cash used in investing activities

For the six months ended June 30, 2025, net cash used in investing activities was $29.1 million compared to net cash used in investing activities of $32.6 million for the same period in 2024. This decrease in cash used was primarily due to a $17.2 million decrease in cash used to purchase marketable securities and a $0.5 million decrease in cash used to purchase property and equipment. These decreases in cash used were partially offset by a $14.3 million decrease in cash provided by the sales and maturities of marketable securities.

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Net cash provided by financing activities

For the six months ended June 30, 2025, net cash provided by financing activities was $48.4 million compared to $0.1 million for the same period in 2024. This increase in cash provided was due to $46.8 million of net proceeds from the January 2025 Registered Direct Offering and $1.6 million of proceeds from the exercise of stock options. Further information regarding the January 2025 Registered Direct Offering can be found below.

Liquidity Outlook

Since our inception, we have funded our operations primarily with proceeds from the issuance of equity to private investors, as well as with the proceeds received from the closing of the Business Combination. Additionally, we began to generate revenue during 2023 from commercial sales of our Platinum instrument. Our primary uses of liquidity have been operating expenses, capital expenditures and our acquisition of certain assets. Cash flows from operations have been historically negative as we continue to invest in the development of our technology in NGPS. Going forward, we anticipate debt or equity offerings will be the primary source of funds to support our operating needs and capital expenditures until we reach scale of our commercial operations. We expect to incur negative operating cash flows on an annual basis for the foreseeable future until such time that we can scale our revenue growth.

We expect that our existing cash and cash equivalents and investments in marketable securities, together with revenue from the sale of our products and services, will be sufficient to meet our liquidity, capital expenditure, and anticipated working capital requirements and fund our operations for at least the next 12 months. We expect to use our cash and cash equivalents and investments in marketable securities and funds from revenue generated to invest in our continued commercialization efforts, to further invest in research and development, for other operating expenses, business acquisitions and for working capital and general corporate purposes.

As of June 30, 2025, we had cash and cash equivalents and investments in marketable securities totaling $214.2 million. Our future capital requirements may vary from those currently planned and will depend on various factors including the pace and success of product commercialization.

Our ongoing commercialization of our Platinum line of instruments as well as our continuing research and development efforts to enhance our instruments may require an accelerated amount of spending to enhance the sales and marketing teams, continue to drive development, and build inventory. Other factors that could accelerate cash needs include: (i) delays in achieving scientific and technical milestones, (ii) unforeseen capital expenditures and fabrication costs related to manufacturing for commercialization, (iii) changes we may make in our business or commercialization strategy, (iv) costs of running a public company, (v) other items affecting our forecasted level of expenditures and use of cash resources, including potential acquisitions, and (vi) increased product and service costs.

On August 11, 2023, we filed a universal shelf registration statement on Form S-3 (the “Shelf Registration Statement”), which became effective on August 22, 2023, covering the offering of Class A common stock, preferred stock, debt securities, warrants, rights and units. After the closing of the July 2025 Registered Direct Offering described below, the remaining capacity of the Shelf Registration Statement is approximately $13.8 million.

On December 11, 2024, we entered into an Equity Distribution Agreement (the “Sales Agreement”) with Canaccord Genuity LLC (“Canaccord”) to sell shares of our Class A common stock, par value $0.0001, having an aggregate offering price of up to $75.0 million, from time to time through an “at-the-market” offering program under which Canaccord will act as sales agent. We have no obligation to sell any shares under the Sales Agreement and may at any time suspend solicitation and offers under the EDA. The ATM Offering is being made pursuant to our shelf registration and a prospectus supplement related to the ATM Offering dated December 11, 2024. During the year ended December 31, 2024, we sold and issued 23,425,650 shares of our Class A common stock under the ATM Offering, resulting in gross proceeds of $36.2 million. Net proceeds were $34.8 million after commissions and issuance costs of $1.4 million. We sold no shares of our Class A common stock under the ATM Offering during the three and six months ended June 30, 2025. In connection with the July 2025 Registered Direct Offering, as described below, the Company provided written notice, effective as of July 3, 2025, to Canaccord Genuity LLC of its election to terminate the Sales Agreement for the Company’s at-the-market offering. At the time of termination, the Company had sold 23,425,650 shares of its Class A common stock under the equity distribution agreement for aggregate gross proceeds of $36.2 million.

On January 3, 2025, we entered into a securities purchase agreement with certain institutional investors pursuant to which we agreed to issue and sell, in a registered direct offering (the “January 2025 Registered Direct Offering”) an aggregate of

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15,625,000 shares of our Class A common stock at a price of $3.20 per Share. The gross proceeds from the January 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds recorded during the six months ended June 30, 2025 were approximately $46.8 million.

On July 3, 2025, the Company entered into a securities purchase agreement with a certain institutional investor pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “July 2025 Registered Direct Offering”), an aggregate of (i) 18,200,000 shares of the Company’s Class A common stock at a price of $1.67 per share and (ii) pre-funded warrants to purchase 11,740,119 shares of common stock (the “Pre-Funded Warrants”). Each of the Pre-Funded Warrants is exercisable for one share of Class A common stock at the exercise price of $0.0001 per Pre-Funded Warrant share. The Pre-Funded Warrants are immediately exercisable and may be exercised at any time until all of the Pre-Funded Warrants issued in the July 2025 Registered Direct Offering are exercised in full. The gross proceeds to the Company from the July 2025 Registered Direct Offering were approximately $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds were approximately $46.9 million.

In the future, we may be unable to obtain any required additional financing on terms favorable to us, if at all. If adequate funds are not available to us on acceptable terms or otherwise, we may be unable to successfully develop or enhance products and services, respond to competitive pressure or take advantage of acquisition opportunities, any of which could have a material adverse effect on our business, financial condition, operating results and cash flows.

Contractual Obligations

We lease certain facilities and equipment under non-cancellable lease agreements that expire at various dates through 2032. As of June 30, 2025, future lease payments, before adjustments for tenant incentives, were approximately $24.4 million.

Licenses related to certain intellectual property

We license certain intellectual property, some of which may be utilized in our current or future product offerings. To preserve the right to use such intellectual property, we are required to make annual minimum fixed payments totaling approximately $0.2 million as well as royalties based on net sales if the royalties exceed annual minimum fixed payments.

Critical Accounting Policies and Significant Judgments and Estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our Condensed Consolidated Financial Statements, which have been prepared in accordance with U.S. GAAP. The preparation of these Condensed Consolidated Financial Statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the Condensed Consolidated Financial Statements, as well as expenses incurred during the reporting periods. Our estimates are based on historical experience and various other factors we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about items not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions. Please refer to our critical accounting policies as disclosed in our Annual Report on Form 10-K for the year ended December 31, 2024 and Note 2. Summary of Significant Accounting Policies, in the accompanying notes to the Condensed Consolidated Financial Statements for a complete description of our significant accounting policies.

Recently Issued Accounting Pronouncements

Please refer to Note 2. Summary of Significant Accounting Policies, in the accompanying notes to the unaudited Condensed Consolidated Financial Statements included elsewhere in this Quarterly Report on Form 10-Q for a description of recently issued accounting pronouncements that may potentially impact our financial position and results of operations.

Item 3.    Quantitative and Qualitative Disclosures About Market Risk

Inflation risk

We believe inflation can and has had an impact on the underlying cost of our supplies and manufacturing components related to our business. To the extent our costs are impacted by general inflationary pressures, we may not be able to fully

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offset such higher costs through price increases or manufacturing efficiencies. Our inability or failure to do so could harm our business, financial condition, results of operations or cash flows.

Interest rate risk

As of June 30, 2025, our marketable securities are comprised primarily of investments in money market funds backed by U.S. government issued securities, U.S. Treasury bills, and high-quality corporate commercial paper. The primary objective of our investments is the preservation of capital to fulfill liquidity needs. We do not enter into investments for trading or speculative purposes. Based on the short-term nature of our holdings, future interest rate changes are not expected to have a material impact on our marketable securities.

Foreign Currency Risk

Presently, we operate our business primarily within the United States, with limited sales outside the United States. To date, we have executed the majority of our transactions in U.S. dollars. In the future, we anticipate expanding into Europe and other locations outside the United States. This expansion may include transacting business in currencies other than the U.S. Dollar. Despite this, we anticipate conducting limited activity outside the U.S. Dollar in the near term, and therefore foreign currency translation risk is not expected to have a material impact on our Condensed Consolidated Financial Statements. However, the growth of our operations, scope of transactions outside the United States, and the use of currencies other than the U.S. Dollar may grow in the future, at which point it is possible foreign currency translation will have a material effect on our operations. To date, we have not entered into any hedging arrangements with respect to foreign currency risk. As our international operations grow, we will continue to reassess our approach to managing our risk relating to fluctuations in currency rates.

Item 4.    Controls and Procedures

Evaluation of Disclosure Controls and Procedures

Under the supervision and with the participation of our management, including our principal executive officer and principal financial officer, we conducted an evaluation of the effectiveness of the design and operation of our disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act.

Disclosure controls and procedures are controls and other procedures that are designed to ensure that information required to be disclosed in our reports filed or submitted under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include controls and procedures designed to ensure that information required to be disclosed in our reports filed under the Exchange Act is accumulated and communicated to management, including our Chief Executive Officer and Chief Financial Officer, to allow timely decisions regarding required disclosure. Based on the evaluation of our disclosure controls and procedures, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures were effective as of June 30, 2025.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting during the quarter ended June 30, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II - OTHER INFORMATION

ITEM 1.    LEGAL PROCEEDINGS.

From time to time, the Company is engaged in legal proceedings in the ordinary course of business. For further information on the Company’s legal proceedings, please refer to Note 17. Commitments and Contingencies, in the notes to the Condensed Consolidated Financial Statements.

ITEM 1A. RISK FACTORS.

Our business, results of operations, financial condition and cash flows are subject to various risks and uncertainties including the risk factors described under the caption “Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2024, as filed with the SEC on March 3, 2025 and in our Quarterly Report on Form 10-Q for the quarter ended March 31, 2025, filed with the SEC on May 15, 2025. We may disclose changes to risk factors or additional risk factors from time to time in our future filings with the SEC.

ITEM 2.    UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS.

Unregistered Sales of Equity Securities and Use of Proceeds

Not applicable.

Issuer Purchases of Equity Securities

Not applicable.

ITEM 3.    DEFAULTS UPON SENIOR SECURITIES.

Not applicable.

ITEM 4.    MINE SAFETY DISCLOSURES.

Not applicable.

ITEM 5.    OTHER INFORMATION.

10b5-1 Trading Arrangements

During the quarter ended June 30, 2025, no officers or directors, as defined in Rule 16a-1(f), adopted, modified or terminated a “Rule 10b5-1 trading arrangement” or a “non-Rule 10b5-1 trading arrangement,” as defined in Item 408 of Regulation S-K.

Delaware Stockholder Litigation

On July 22, 2025, the Company and the other parties of a putative class action lawsuit that was filed on May 16, 2024 in the Delaware Court of Chancery, styled Farzad HighCape Capital, et al. (the “Delaware Stockholder Litigation”), through a mediation process, reached a preliminary settlement. As a result, as of June 30, 2025, the Company recorded a gross Accrued legal settlement liability of $8.0 million and a $4.6 million Legal settlement insurance receivable in the Condensed Consolidated Balance Sheets and associated legal settlement fees of $3.4 million in Legal settlement, net of insurance, in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Of the $8.0 million accrued liability, $7.6 million represents the preliminary settlement amount and $0.4 million is an estimate of legal and related expenses to finalize the legal settlement. The preliminary legal settlement is subject to execution of definitive documentation and a number of court procedural processes, including notice to and approval of the class members, and final court approval. For further information on the Delaware Stockholder Litigation, please refer to Note 17. Commitments and Contingencies, in the notes to the Condensed Consolidated Financial Statements.

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ITEM 6.    EXHIBITS.

The following exhibits are filed as part of, or incorporated by reference into, this Quarterly Report on Form 10-Q.

Exhibit Number

Exhibit Description

Filed Herewith

Incorporated by Reference Herein from Form or Schedule

Filing Date

3.1

Second Amended and Restated Certificate of Incorporation of Quantum-Si Incorporated, as amended.

Form 10-Q (Exhibit 3.1)

8/7/2024

3.2

Amended and Restated Bylaws of Quantum-Si Incorporated

Form 10-K (Exhibit 3.2)

3/1/2021

10.1

Form of Securities Purchase Agreement, by and among Quantum-Si Incorporated and the Purchaser.

Form 8-K (Exhibit 10.1)

7/7/2025

10.2

Form of Placement Agency Agreement between the Company and the Placement Agent.

Form 8-K (Exhibit 10.2)

7/7/2025

31.1

Certification of the Principal Executive Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

X

31.2

Certification of the Principal Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

X

32.1*

Certification of the Principal Executive Officer pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

X

32.2*

Certification of the Principal Financial Officer pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

X

101.INS

Inline XBRL Instance Document (the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document)

X

101.SCH

Inline XBRL Taxonomy Extension Schema Document

X

104

Cover Page Interactive Data File (embedded within the Inline XBRL document)

X

*The certifications attached as Exhibit 32.1 and 32.2 that accompany this Quarterly Report on Form 10-Q are not deemed filed with the Securities and Exchange Commission and are not to be incorporated by reference into any filing of Quantum-Si Incorporated under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as

amended (whether made before or after the date of such Form 10-Q), irrespective of any general incorporation language contained in such filing.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

			QUANTUM-SI INCORPORATED
Date: August 5, 2025			By:			/s/ Jeffrey Hawkins
						Jeffrey Hawkins
						President and Chief Executive Officer
Date: August 5, 2025			By:			/s/ Jeffry Keyes
						Jeffry Keyes
						Chief Financial Officer and Treasurer

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FAQ

What were Quantum-Si (QSI) revenues for the six months ended June 30, 2025?

Total revenue for the six months ended June 30, 2025 was $1.433 million (product $1.366M; service $67K).

How large was Quantum-Si's net loss and loss per share in H1 2025?

Net loss for the six months ended June 30, 2025 was $48.0 million, and basic and diluted net loss per share was $0.26.

What liquidity does Quantum-Si report as of June 30, 2025?

As of June 30, 2025 the Company reported cash and cash equivalents of $22.188M and marketable securities of $192.023M (total ~$214.2M); management expects this to fund operations for at least 12 months from issuance date.

Did Quantum-Si record any material legal or contingent liabilities in Q2 2025?

Yes. The Company recorded an accrued legal settlement liability of $8.0M and a related legal settlement insurance receivable of $4.638M as of June 30, 2025; the settlement is described as preliminary and subject to final documentation and court approval.

What financing did Quantum-Si complete in early 2025?

On January 3, 2025 the Company completed a registered direct offering of 15,625,000 Class A shares at $3.20 per share with gross proceeds of $50.0M and net proceeds of approximately $46.8M.

What are the Company’s main expense drivers?

For H1 2025, the primary expense drivers were Research & Development $28.93M and Selling, General & Administrative $23.78M.