Bionano Genomics, Inc. 10-Q

ITEM 1. FINANCIAL STATEMENTS BIONANO GENOMICS, INC. Condensed Consolidated Balance Sheets (Unaudited) March 31, 2025 December 31, 2024 Assets Current assets: Cash and cash equivalents $ 3,625,000 $ 9,173,000 Investments 14,606,000 302,000 Accounts receivable, net 3,354,000 4,752,000 Inventory 9,562,000 11,121,000 Prepaid expenses and other current assets 2,782,000 3,141,000 Restricted investments 11,000,000 11,000,000 Total current assets 44,929,000 39,489,000 Restricted cash — 400,000 Property and equipment, net 18,339,000 19,219,000 Operating lease right-of-use assets 1,108,000 1,804,000 Finance lease right-of-use assets 3,249,000 3,299,000 Intangible assets, net 8,365,000 9,705,000 Other long-term assets 2,424,000 2,754,000 Total assets $ 78,414,000 $ 76,670,000 Liabilities and stockholders’ equity Current liabilities: Accounts payable 6,562,000 6,962,000 Accrued expenses 3,937,000 5,641,000 Contract liabilities 1,020,000 1,128,000 Operating lease liability 1,592,000 2,991,000 Finance lease liability 257,000 260,000 Convertible debentures and High Trail Notes payable (at fair value) 13,040,000 20,362,000 Total current liabilities 26,408,000 37,344,000 Operating lease liability, net of current portion — 145,000 Finance lease liability, net of current portion 3,526,000 3,539,000 Long-term contract liabilities 292,000 267,000 Total liabilities $ 30,226,000 $ 41,295,000 Commitments and contingencies (Note 7) Stockholders’ equity: Preferred stock, $ 0.0001 par value; 10,000,000 shares authorized at March 31, 2025 and December 31, 2024; no shares issued and outstanding at March 31, 2025 and December 31, 2024 — — Common stock, $ 0.0001 par value, 400,000,000 shares authorized at March 31, 2025 and December 31, 2024; 3,101,400 and 1,865,400 shares issued and outstanding at March 31, 2025 and December 31, 2024, respectively — — Additional paid-in capital 744,501,000 728,573,000 Accumulated deficit ( 696,327,000 ) ( 693,225,000 ) Accumulated other comprehensive income 14,000 27,000 Total stockholders’ equity $ 48,188,000 $ 35,375,000 Total liabilities and stockholders’ equity $ 78,414,000 $ 76,670,000 See accompanying notes to the unaudited condensed consolidated financial statements. 3 Table of Contents BIONANO GENOMICS, INC. Condensed Consolidated Statements of Operations (Unaudited) Three Months Ended March 31, 2025 2024 Revenue: Product revenue $ 6,004,000 $ 6,828,000 Service and other revenue 453,000 1,941,000 Total revenue 6,457,000 8,769,000 Cost of revenue: Cost of product revenue 3,053,000 4,904,000 Cost of service and other revenue 466,000 1,041,000 Total cost of revenue 3,519,000 5,945,000 Operating expenses: Research and development 2,370,000 9,779,000 Selling, general and administrative 9,033,000 19,088,000 Intangible assets and other long-lived assets impairment — 448,000 Restructuring costs — 4,632,000 Total operating expenses 11,403,000 33,947,000 Loss from operations ( 8,465,000 ) ( 31,123,000 ) Other income (expense): Interest income 290,000 1,044,000 Other income (expense) 5,080,000 ( 1,361,000 ) Total other income (expense) 5,370,000 ( 317,000 ) Loss before income taxes ( 3,095,000 ) ( 31,440,000 ) Benefit (provision) for income taxes ( 7,000 ) 18,000 Net loss $ ( 3,102,000 ) $ ( 31,422,000 ) Net loss per share, basic and diluted $ ( 1.15 ) $ ( 35.75 ) Weighted-average common shares outstanding basic and diluted 2,694,000 879,000 See accompanying notes to the unaudited condensed consolidated financial statements. 4 Table of Contents BIONANO GENOMICS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) Three Months Ended March 31, 2025 2024 Net loss: $ ( 3,102,000 ) $ ( 31,422,000 ) Other comprehensive loss: Unrealized loss on investment securities ( 3,000 ) ( 13,000 ) Foreign currency translation adjustments ( 10,000 ) ( 26,000 ) Other comprehensive loss $ ( 13,000 ) $ ( 39,000 ) Total comprehensive loss $ ( 3,115,000 ) $ ( 31,461,000 ) See accompanying notes to the unaudited condensed consolidated financial statements. 5 Table of Contents BIONANO GENOMICS, INC. Condensed Consolidated Statements of Stockholders’ Equity (Deficit) (Unaudited) Common Stock Additional Paid-in Capital Accumulated Deficit Accumulated Other Comprehensive Income (Loss) Total Stockholders’ Equity (Deficit) Shares Amount Balance at January 1, 2024 762,600 $ — $ 677,342,000 $ ( 581,208,000 ) $ 23,000 $ 96,157,000 Stock-based compensation expense — — 3,015,000 — — 3,015,000 Issue common stock, net of issuance costs 196,300 — 15,059,000 — — 15,059,000 Net loss — — — ( 31,422,000 ) — ( 31,422,000 ) Other comprehensive loss — — — ( 39,000 ) ( 39,000 ) Balance at March 31, 2024 958,900 $ — $ 695,416,000 $ ( 612,630,000 ) $ ( 16,000 ) $ 82,770,000 Balance at January 1, 2025 1,865,400 $ — $ 728,573,000 $ ( 693,225,000 ) $ 27,000 $ 35,375,000 Stock-based compensation expense — — 1,587,000 — — 1,587,000 Issue common stock and warrants, net of issuance costs 934,000 — 13,982,000 — — 13,982,000 Issue stock for warrant exercises 280,000 — 9,000 — — 9,000 Issuance of common stock for convertible debentures payable 22,000 — 350,000 — — 350,000 Net loss — — — ( 3,102,000 ) — ( 3,102,000 ) Other comprehensive loss — — — — ( 13,000 ) ( 13,000 ) Balance at March 31, 2025 3,101,400 $ — $ 744,501,000 $ ( 696,327,000 ) $ 14,000 $ 48,188,000 See accompanying notes to the unaudited condensed consolidated financial statements. 6 Table of Contents BIONANO GENOMICS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) Three Months Ended March 31, 2025 2024 Operating activities: Net loss $ ( 3,102,000 ) $ ( 31,422,000 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization expense 2,434,000 3,007,000 Amortization of financing lease right-of-use asset 51,000 51,000 Accretion of interest on securities ( 242,000 ) ( 694,000 ) Non-cash lease expense 120,000 27,000 Gain on lease termination/modification ( 397,000 ) ( 73,000 ) Net realized loss on investments — 2,000 Stock-based compensation 1,587,000 3,015,000 Change in fair value of contingent consideration — ( 640,000 ) Change in fair value of convertible debentures, convertible notes payable and option liability ( 5,472,000 ) ( 7,534,000 ) Intangible assets and other long-lived assets impairment — 448,000 Disposal of property and equipment 19,000 284,000 Cost of leased equipment sold to customer 215,000 98,000 Changes in operating assets and liabilities: Accounts receivable 1,398,000 1,004,000 Inventory 1,110,000 ( 200,000 ) Prepaid expenses and other current assets 74,000 1,073,000 Other assets 330,000 786,000 Accounts payable ( 401,000 ) ( 537,000 ) Accrued expenses and contract liabilities ( 488,000 ) 3,174,000 Net cash used in operating activities ( 2,764,000 ) ( 28,131,000 ) Investing Activities: Purchases of property and equipment — ( 26,000 ) Purchase of available for sale securities ( 64,767,000 ) ( 110,557,000 ) Sale and maturity of available for sale securities 50,701,000 158,169,000 Net cash (used in)/provided by investing activities ( 14,066,000 ) 47,586,000 Financing activities: Principal payments on financing lease liability ( 16,000 ) ( 13,000 ) Proceeds from sale of common stock and warrants 13,317,000 15,445,000 Offering expenses on sale of common stock and warrants ( 919,000 ) ( 386,000 ) Proceeds from warrant exercises 9,000 — Payments on High Trail Notes — ( 36,664,000 ) Payments on convertible debentures ( 1,500,000 ) — Net cash provided by/(used in) financing activities 10,891,000 ( 21,618,000 ) Effect of exchange rates on cash, cash equivalents and restricted cash ( 9,000 ) ( 26,000 ) Net decrease in cash, cash equivalents and restricted cash ( 5,948,000 ) ( 2,189,000 ) Cash, cash equivalents and restricted cash at beginning of period 9,573,000 18,348,000 Cash, cash equivalents and restricted cash at end of period $ 3,625,000 $ 16,159,000 Reconciliation of cash, cash equivalents and restricted cash reported within the unaudited condensed consolidated balance sheets to the total amounts reported on the unaudited condensed consolidated statements of cash flows Cash and cash equivalents 3,625,000 15,759,000 7 Table of Contents Restricted cash — 400,000 Total cash, cash equivalents and restricted cash at end of period $ 3,625,000 $ 16,159,000 Supplemental cash flow disclosures: Cash paid for interest $ 479,000 $ 5,620,000 Cash paid for operating lease liabilities $ 816,000 $ 669,000 Supplemental disclosure of non-cash investing and financing activities: Transfer of instruments and servers from inventory to property and equipment, net $ 449,000 $ 3,505,000 Debt issuance costs included in accounts payable $ — $ 44,000 Issuance of common stock for convertible debentures payable $ 350,000 $ — Fees paid in common stock $ 1,584,000 $ — See accompanying notes to the unaudited condensed consolidated financial statements. 8 Table of Contents BIONANO GENOMICS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) 1. Organization and Basis of Presentation Description of Business Bionano Genomics, Inc. (collectively, with its consolidated subsidiaries, the “Company”) is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Company offers optical genome mapping (“OGM”) solutions, diagnostic services and software for applications across basic, translational and clinical research, and for other applications including bioprocessing. The Company offers a platform-agnostic software solution, which integrates next-generation sequencing, microarray and OGM data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. The Company also offers nucleic acid extraction and purification solutions using proprietary isotachophoresis (“ITP”) technology. Through its wholly-owned subsidiary, Lineagen Inc. (doing business as Bionano Laboratories), the Company also provides OGM-based diagnostic testing services. Reverse Stock Split On January 24, 2025, the Company filed a Certificate of Amendment to its Amended and Restated Certificate of Incorporation with the Secretary of State of the State of Delaware to effect a reverse stock split of all issued and outstanding shares of the Company’s common stock at a ratio of 1-for-60. The reverse stock split did not change the par value or the authorized number of shares of the Company’s common stock. The Company’s condensed consolidated financial statements and notes to the condensed consolidated financial statements present the retroactive effect of the reverse stock split on the Company’s common stock and per share amounts for all periods presented. Basis of Presentation The accompanying financial information has been prepared by the Company pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”) for interim reporting purposes. The condensed consolidated financial statements are unaudited. The unaudited condensed consolidated financial statements reflect, in the opinion of the Company’s management, all adjustments, consisting of only normal recurring adjustments, necessary for a fair presentation of financial position, results of operations, changes in equity, and comprehensive loss and cash flows for each period presented in accordance with United States generally accepted accounting principles (“U.S. GAAP”). All intercompany transactions and balances have been eliminated. The operating results presented in these unaudited interim condensed financial statements are not necessarily indicative of the results that may be expected for any future periods. These interim unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024. Reclassifications Certain amounts reported in prior years have been reclassified to conform with the presentation in the current year. These reclassifications had no effect on the reported results of operations. Liquidity and Going Concern The Company has experienced recurring net losses from operations and negative cash flows from operating activities since its inception, has a significant accumulated deficit and expects to continue to incur net losses into the foreseeable future. As of March 31, 2025, the Company had approximately $ 3.6 million in cash and cash equivalents, $ 14.6 million in short-term investments, $ 11.0 million in restricted short-term investments and working capital of $ 18.5 million. The amount the Company is required to hold as restricted cash or investments is equal to the lesser of (a) $ 11.0 million and (b) the then outstanding principal balance of the Debentures (as defined in Note 5 (Debt) in these notes accompanying the unaudited condensed consolidated financial statements). As of March 31, 2025 the Company had $ 13.6 million of principal outstanding under the Debentures (see Note 5 (Debt) to our unaudited condensed consolidated financial statements) and an accumulated deficit of $ 696.3 million. During the three months ended March 31, 2025, the Company used $ 2.8 million of cash in operations. Management expects operating losses and negative cash flows to continue for at least the next year as the Company continues to incur costs related to product development and commercialization efforts. Management has prepared cash flows forecasts which indicate that based on the Company’s expected operating losses and negative cash flows, there is substantial doubt about the Company’s ability to continue as a going concern within 12 months after the date that the unaudited condensed consolidated financial statements for the three months ended March 31, 2025, are issued. Management’s ability to continue as a going concern is dependent upon its ability to raise additional funding. Management’s plans to raise additional capital to fulfill its operating and capital requirements for at least 12 months include public or private equity or debt financings. However, the 9 Table of Contents Company may not be able to secure such financing in a timely manner or on favorable terms, if at all, and if the Company is unable to raise sufficient additional capital in the very near term, it may need to further curtail or cease operations and seek protection by filing a voluntary petition for relief under the United States Bankruptcy Code. Furthermore, if the Company issues equity securities to raise additional funds, its existing stockholders may experience dilution, and the new equity securities may have rights, preferences and privileges senior to those of the Company’s existing stockholders. The unaudited condensed consolidated financial statements have been prepared on a going concern basis, which contemplates the realization of assets and settlement of liabilities in the normal course of business, and do not include any adjustments to reflect the outcome of this uncertainty. Significant Accounting Policies During the three months ended March 31, 2025, there were 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. Restructuring Expenses The Company’s restructuring expense consists primarily of actions taken in May and October 2023 (the “2023 Workforce Reductions”) and March and September 2024 (the “2024 Workforce Reductions”) in order to reduce costs and improve operations and manufacturing efficiency. Severance-related costs were accounted for as a one-time termination benefit communicated by period end without an additional service component, so the charge represents the total amount expected to be incurred. As a result of reducing facility costs and discretionary spending unrelated to headcount and combined with the cost savings from the 2023 Workforce Reductions and 2024 Workforce Reductions, such plans were intended to decrease expenses and maintain a streamlined organization to support the Company’s business. In connection with the Company’s restructuring initiatives, the Company entered into a lease termination agreement on February 28, 2024 with the landlord for the facility in Salt Lake City that resulted in a one-time termination fee of approximately $ 0.2 million in the first quarter of 2024. The Company continued to lease the property through June 2024. The Company accounted for the lease amendment as a lease modification and recorded a gain of $ 0.1 million during the three months ended March 31, 2024. On March 1, 2024, and September 4, 2024, the Company’s board of directors approved restructuring plans, including reductions in force, that was expected to reduce the Company’s annualized operating expenses. The 2024 Workforce Reductions were incremental to the 2023 Workforce Reductions. As part of the 2024 Workforce Reductions, the Company reduced its overall headcount by approximately 120 and 83 employees in March and September 2024, respectively. The Company had completed the reduction in force from the 2024 Workforce Reductions as of December 31, 2024. In addition, as part of the 2024 Workforce Reductions, Bionano Laboratories phased out the offering of certain testing services related to neurodevelopmental disorders, including autism spectrum disorders, and other disorders of childhood development. The Company may also incur additional costs not currently contemplated due to events that may occur as a result of, or that are associated with, the reductions in force. See Note 7 (Commitments and Contingencies in these notes accompanying the unaudited condensed consolidated financial statements) for additional information. Impairment of Long-Lived Assets (including Finite-Lived Intangible Assets) Long-lived assets are reviewed for impairment if indicators of potential impairment exist. If the Company identifies a change in the circumstances related to its long-lived assets, such as property and equipment and intangible assets (other than goodwill), that indicates the carrying value of any such asset may not be recoverable, the Company will perform an impairment analysis. A long-lived asset (other than goodwill) is not recoverable when the undiscounted cash flows expected to be generated by the asset (or asset group) are less than the asset’s carrying amount. Any required impairment loss would be measured as the amount 10 Table of Contents by which the asset’s carrying value exceeds its fair value, and would be recorded as a reduction in the carrying value of the related asset and a charge to operating expense. During the three months ended March 31, 2024, the Company experienced a triggering event as a result of the restructuring initiatives announced in March 2024 that required an evaluation of its non-OGM Bionano Laboratories asset group for impairment. The Company performed a recoverability test and concluded that the non-OGM Bionano Laboratories long-lived assets were not recoverable; therefore, the Company measured the impairment loss and fully impaired the intangible assets acquired through the acquisition of Lineagen, consisting of its trade name and customer relationship intangible assets. The Company recognized an impairment loss of $ 0.4 million during the three months ended March 31, 2024. No impairment losses were recorded during the three months ended March 31, 2025. Inventories The Company reviews its inventories for classification purposes. The value of inventories not expected to be realized in cash, sold or consumed during the next 12 months are classified as non-current within other long-term assets. As of March 31, 2025, $ 1.9 million of inventories were included in other long-term assets. Loss on disposal of property and equipment Loss on disposal of property and equipment includes the net book value of assets that have been abandoned or retired and consists primarily of our leasehold improvements, furniture, equipment and fixtures that were abandoned and disposed of in the normal course of business. We recorded an immaterial loss on disposal of property and equipment during the three months ended March 31, 2025 and $ 0.3 million during the three months ended March 31, 2024. Change in depreciable lives of property and equipment The Company reviews the estimated useful life of its fixed assets on an ongoing basis. This review indicated that the actual lives of the Company’s Saphyr® and Stratys™ instruments were longer than the estimated useful lives used for depreciation purposes in the Company’s unaudited condensed consolidated financial statements. As a result, effective January 1, 2024, the Company changed its estimates of the useful lives of the Company’s Saphyr and Stratys instruments to better reflect the estimated period during which these assets will remain in service. The estimated useful lives of the Company’s Saphyr and Stratys instruments were increased from 5 to 7 years. The effect of this change in estimate reduced depreciation expense by $ 1.8 million for the fiscal year 2024. There were no changes to the depreciable lives of property and equipment during the three months ended March 31, 2025. Segment Reporting Operating segments are defined as components of an entity for which separate financial information is available and that is regularly reviewed by the Chief Operating Decision Maker (“CODM”) in deciding how to allocate resources to an individual segment and in assessing performance. The Company’s CODM is its Chief Executive Officer. The Company has determined it has one operating and reportable segment. Segment information is consistent with how management reviews the business, makes investing and resource allocation decisions and assesses operating performance. The Company’s measure of segment performance on a consolidated basis is consolidated net loss. The measure of segment assets is reported on the unaudited condensed consolidated balance sheets as total assets. Refer to the unaudited condensed consolidated statements of operations and comprehensive loss for the Company’s measure of profit (loss). See Note 9 (Segment Reporting) in these notes accompanying the unaudited condensed consolidated financial statements for additional information. Recently Adopted Accounting Pronouncements In November 2023, the FASB issued Accounting Standards Update, or ASU, 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures , which updates reportable segment disclosure requirements primarily through enhanced disclosures about significant segment expenses for all public entities, including public entities with a single reportable segment. On an annual and interim basis, entities are required to disclose significant segment expenses that are regularly provided to the CODM. The ASU is effective for fiscal years beginning after December 15, 2023 and interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The Company adopted the new standard in the fourth quarter of 2024 which did not have a material impact on its consolidated financial statements. See Note 9 (Segment Reporting) in these notes accompanying the unaudited condensed consolidated financial statements for disclosures related to the Company’s segment reporting. Recently Issued Accounting Pronouncements In December 2023, the FASB issued ASU 2023-09, Income Taxes (Topic 740): Improvement to Income Tax Disclosures to enhance the transparency and decision usefulness of income tax disclosures. Two primary enhancements related to this ASU include disaggregating existing income tax disclosures relating to the effective tax rate reconciliation and income taxes paid. ASU 2023-09 is effective for annual periods beginning after December 15, 2024 on a prospective basis. Early adoption is 11 Table of Contents permitted. The Company is currently evaluating the impact of this accounting standard update on the Company’s consolidated financial statements and related disclosures. In November 2024, the FASB issued ASU 2024-03, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses , which requires additional disclosure about specific expense categories in the notes to financial statements. The amendments are effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments should be applied either prospectively to financial statements issued for reporting periods after the effective date of this ASU or retrospectively to any or all prior periods presented in the financial statements. The Company is currently evaluating the impact of this accounting standard update on the Company’s consolidated financial statements and related disclosures. 2. Net Loss Per Share Basic net loss per share is calculated by dividing the net loss by the weighted-average number of common shares outstanding for the period. Diluted net loss per share is computed by dividing the net loss by the weighted average number of common shares and common share equivalents outstanding for the period. Common share equivalents are only included when their effect is dilutive. The Company’s potentially dilutive securities which include outstanding convertible debentures and High Trail Notes (as defined in Note 5), outstanding common warrants to purchase common stock, restricted stock units (“RSUs”), performance stock units (“PSUs”), and outstanding stock options under the Company’s equity incentive plans have been excluded from the computation of diluted net loss per share as they would be anti-dilutive to the net loss per share. For all periods presented, there is no difference in the number of shares used to calculate basic and diluted shares outstanding due to the Company’s net loss position. Potentially dilutive securities not included in the calculation of diluted net loss per share because to do so would be anti-dilutive were as follows (in common stock equivalent shares): March 31, 2025 March 31, 2024 Common stock options 169,000 51,000 Common warrants 2,080,700 362,000 Convertible debentures and High Trail Notes 842,000 142,000 RSUs 5,210 3,000 PSUs — 480 Total 3,096,910 558,480 3. Revenue Recognition Revenue by Source Three Months Ended March 31, 2025 2024 Instruments $ 689,000 $ 1,614,000 Consumables 3,247,000 3,464,000 Software 2,068,000 1,750,000 Total product revenue 6,004,000 6,828,000 Service and other 453,000 1,941,000 Total revenue $ 6,457,000 $ 8,769,000 Revenue by Geographic Location Three Months Ended March 31, 2025 2024 $ % $ % Americas $ 3,058,000 47.4 % $ 4,690,000 53.5 % EMEA 3,066,000 47.5 % 3,133,000 35.7 % Asia Pacific 333,000 5.2 % 946,000 10.8 % Total $ 6,457,000 100 % $ 8,769,000 100 % 12 Table of Contents The table above provides revenue from contracts with customers by source and geographic region (based on the customer’s billing address) on a disaggregated basis. Americas consists of North America and South America. EMEA consists of Europe, the Middle East, and Africa. Asia Pacific includes China, Japan, South Korea, Singapore, India and Australia. For the three months ended March 31, 2025 and 2024, the United States represented 38.4 % and 42.6 % of total revenue, respectively. No other countries represented greater than 10% of total revenue during the three months ended March 31, 2025 and 2024. Remaining Performance Obligations As of March 31, 2025, the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied was approximately $ 1.3 million. These remaining performance obligations primarily relate to extended warranty, support and maintenance obligations, as well as obligations related to software under hosting arrangements. The Company expects to recognize approximately 69.9 % of this amount as revenue during the remainder of 2025, 19.4 % in 2026, and 10.7 % in 2027 and thereafter. Warranty revenue is included in service and other revenue. The Company recognized revenue of approximately $ 0.7 million and $ 0.6 million during the three months ended March 31, 2025 and 2024, respectively, which was included in the contract liability balance at the end of the year preceding each period . 4. Balance Sheet Account Details Accounts Receivable and Allowance for Credit Losses March 31, 2025 December 31, 2024 December 31, 2023 Accounts receivable, net: Accounts receivable, trade $ 3,462,000 $ 4,909,000 $ 9,802,000 Allowance for credit losses ( 108,000 ) ( 157,000 ) ( 483,000 ) $ 3,354,000 $ 4,752,000 $ 9,319,000 Changes to the allowance for credit losses during the three months ended March 31, 2025 and 2024 were as follows: Allowance for Credit Losses Balance as of January 1, 2024 $ ( 483,000 ) Provision for expected credit loss — Write-offs 55,000 Balance as of March 31, 2024 $ ( 428,000 ) Balance as of January 1, 2025 $ ( 157,000 ) Provision for expected credit loss — Write-offs 49,000 Balance as of March 31, 2025 $ ( 108,000 ) The Company’s analysis included an assessment of aged trade receivables balances and their underlying credit risk characteristics. The Company’s evaluation of past events, current conditions, and reasonable and supportable forecasts about the future resulted in an expectation of immaterial credit losses. 13 Table of Contents Inventory The components of inventories are as follows: March 31, 2025 December 31, 2024 Inventory: Raw materials $ 6,551,000 $ 6,715,000 Work in process 1,563,000 2,349,000 Finished goods 3,303,000 4,212,000 $ 11,417,000 $ 13,276,000 Inventories current $ 9,562,000 $ 11,121,000 Inventories non-current (included in other long-term assets) $ 1,855,000 $ 2,155,000 Intangible Assets Intangible assets that are subject to amortization consisted of the following for the periods presented: March 31, 2025 December 31, 2024 Gross Carrying Amount Accumulated Amortization Net Carrying Amount Gross Carrying Amount Accumulated Amortization Net Carrying Amount Trade name $ 1,000,000 $ ( 692,000 ) $ 308,000 $ 1,000,000 $ ( 642,000 ) $ 358,000 Customer relationships 3,000,000 ( 2,075,000 ) 925,000 3,000,000 ( 1,925,000 ) 1,075,000 Developed technology 22,800,000 ( 15,770,000 ) 7,030,000 22,800,000 ( 14,630,000 ) 8,170,000 Intangibles, net $ 26,800,000 $ ( 18,537,000 ) $ 8,263,000 $ 26,800,000 $ ( 17,197,000 ) $ 9,603,000 Intangible assets not subject to amortization totaled $ 0.1 million at March 31, 2025 and December 31, 2024, and related to the Company’s domain name. See Note 1 (Organization and Basis of Presentation) in these notes accompanying the unaudited condensed consolidated financial statements for further discussion on the impairment charges impacting the Company’s intangible assets in the period. Accrued Expenses Accrued expenses consist of the following: March 31, 2025 December 31, 2024 Compensation expenses $ 1,860,000 $ 1,983,000 Taxes payable 660,000 729,000 Insurance 403,000 16,000 Accrued liability for fees to be paid in common stock — 1,584,000 Professional fees and royalties 307,000 402,000 Warranty liabilities 567,000 276,000 Customer deposits — 17,000 Other 140,000 634,000 Total $ 3,937,000 $ 5,641,000 14 Table of Contents 5. Debt JGB Debentures On May 24, 2024, the Company entered into a securities purchase agreement with certain accredited investors (the “Holders”) and JGB Collateral LLC, as collateral agent for the Holders, for the sale by the Company in a private placement (the “JGB Debentures Offering”) of: • 38,000 shares (the “Shares”) of the Company’s common stock, and • Senior Secured Convertible Debentures in the aggregate principal amount of $ 20.0 million (the “Debentures”), for an aggregate purchase price of $ 18.0 million. The closing of the JGB Debentures Offering occurred on May 24, 2024. In connection with the closing of the JGB Debentures Offering, the Company received net proceeds of approximately $ 16.3 million, after payment of placement agent fees, and other offering expenses. The Company used the proceeds received to fully redeem the outstanding balance due under the High Trail Note of approximately $ 17.6 million, as amended (see “High Trail Agreement & Amendment” below). Debentures The Debentures have an aggregate face value of $ 20.0 million and were issued with an original issue discount of $ 2.0 million. The Debentures mature on May 24, 2026, and have an interest rate of 11 % per annum payable monthly on the last business day of each calendar month. For the three months ended March 31, 2025, the Company had paid the Holders $ 0.4 million in interest, which is included in the change in fair value within other income (expense), net. The Company recorded the Debentures at their fair value at issuance of $ 19.9 million, per the fair value option under ASC 825 (refer to Note 8 (Investments and Fair Value Measurements)) and they will be measured on a recurring basis and adjusted through other income and expense, net. The Shares were recorded at $ 0 in common stock and additional paid in capital, which represents the residual amount after allocation of proceeds to the Debentures at fair value. The Company recognized an initial loss on the issuance of the Debentures of $ 1.9 million for the difference between the fair value of the Debentures and proceeds from the transaction, which was recorded in other income (expense) on the unaudited condensed consolidated statement of operations. The Company incurred debt issuance costs of $ 1.7 million related to the JGB Debentures Offering, which was charged to interest expense and recorded in other income (expense) on the unaudited condensed consolidated statement of operations. The Holders of the Debentures requested that the Company redeem up to $ 1.0 million per calendar month of its Debentures may request redemption up to $ 0.5 million per calendar month beginning in January 2025 to July 2025, and up to $ 1.4 million from August 2025 onward. The table below shows the amount of potential redemptions each year until the maturity of the Debentures as of March 31, 2025. 2025 $ 8,875,000 2026 5,116,000 Total $ 13,991,000 The Company may redeem the Debentures, subject to certain Equity Conditions (as defined in the Debentures), at any time after August 2025 by paying an amount equal to the entire outstanding principal amount of the Debenture, plus all accrued and unpaid interest, plus the applicable Company Redemption Premium (as defined in the Debentures, the “Premium”) plus any other amounts due and payable under the Debentures. The Premium is an amount equal to 112 % of the principal amount of the Debenture if the redemption is prior to the first anniversary of the original issue date, or 106 % of the principal amount of the Debenture if the redemption is on or after the first anniversary of the original issue date. No partial redemptions by the Company are permitted. At the election of the holder, each Debenture is convertible, in whole or in part, at any time and from time to time at a conversion price of $ 16.20 per share of common stock. The conversion price is subject to adjustment for stock dividends, stock splits, and certain other corporate events. Notwithstanding the foregoing, the Company will not effect any conversion under the Debentures to the extent that such conversion would cause the holder’s beneficial ownership of the Company’s common stock to exceed 4.99 % (or 9.99 % at the election of the holder) of the Company’s issued and outstanding common stock. Under the Debentures, the Company must at all times maintain a cash or restricted investments balance equal to the lesser of (a) $ 11.0 million and (b) the then outstanding principal balance of the Debentures, in a blocked account. In addition, for as long as any portion of the Debentures remain outstanding, the Company is generally restricted from: incurring indebtedness; granting or suffering liens on any of its property or assets; amending its organizational documents; repurchasing any of its securities; paying dividends; selling, disposing, licensing or leasing its assets other than in the ordinary course; and other customary restrictive covenants. The Debentures also set forth certain customary events of default after which the Debentures may be 15 Table of Contents declared immediately due and payable, including certain types of bankruptcy or insolvency events of default involving the Company and its subsidiaries, and in the event of a change of control or fundamental transaction as defined in the Debentures. As of March 31, 2025 the Company had $ 13.6 million of principal outstanding, including $ 0.5 million of the “Fill-Up Amount” (as defined in the JGB Amendment). The Fill-Up Amount represents the shares issuable to adjust for stock price volatility between the date of the settlement agreement and the effective date of the resale registration statement registering such shares for issuance. The Fill-Up Amount shall be payable by adding each Holder’s pro rata share of the Fill-Up Amount to its Debenture. Refer to Note 8 (Investments and Fair Value Measurements), for fair value measurements and additional discussion. The activity for the three months ended March 31, 2025 was as follows: Debentures Principal balance, January 1, 2025 $ 15,491,000 Less: Conversions ( 350,000 ) Redemption payments of principal ( 1,500,000 ) Debentures principal balance, March 31, 2025 $ 13,641,000 JGB Amendment On December 31, 2024, the Company entered into an amendment of the Debentures (the “JGB Amendment”) with the Holders thereof. Pursuant to the JGB Amendment, the parties agreed that (i) no amortization payment would be paid in December 2024; (ii) the maximum monthly amortization payments due between January 2025 and July 2025 would be reduced from $ 1.0 million per month to $ 0.5 million per month; (iii) the maximum monthly amortization payments due from August 2025 through repayment in full of the principal aggregate amount would be $ 1.4 million per month; (iv) the conversion price of the Debentures would be reduced from $ 120.00 to $ 16.20 ; and (v) the Debentures would become non-callable by the Company until August 2025. As consideration for the JGB Amendment, the Company issued to the Holders approximately 83,000 shares of its common stock (the “Private Placement Shares”). The Company accounted for the JGB Amendment as a debt extinguishment and recognized a loss on the extinguishment of the convertible debentures payable of $ 7.3 million, which was recorded in other income (expense) on the consolidated statement of operations as of December 31, 2024. On January 3, 2025, the Holders had converted $ 0.4 million principal into approximately 22,000 shares of the Company’s common stock, at the conversion price of $ 16.20 per share (as adjusted for the reverse stock split). High Trail Agreement & Amendment On February 27, 2024, the Company entered into a letter agreement and an Amendment to the Registered Note (the “Note Amendment”), with the Purchaser of the High Trail Notes which provided for, among other things, the following: • Reduction of the minimum available liquidity covenant from $ 50.0 million to $ 25.0 million; • Reduction of the restricted cash covenant from $ 35.0 million to the amount equal to the sum of (i) the outstanding principal amount of the senior secured convertible notes payable due 2025 (the “High Trail Registered Notes”) plus (ii) approximately $ 0.7 million, which will be further reduced as the remaining principal on the High Trail Registered Notes are retired; • Cancellation of the March 2024 partial redemption payment and delay of the April 2024 partial redemption payment; • Redemption of the outstanding $ 17.0 million balance of the privately placed senior secured convertible notes payable due 2025 (the “High Trail Private Placement Notes” and together with the High Trail Registered Notes, the “High Trail Notes”) at a redemption price of 115 % for a total redemption payment of approximately $ 19.6 million; • Redemption of approximately $ 10.7 million of the High Trail Registered Notes at a redemption price of 115 % for a total redemption payment of approximately $ 12.3 million; and • Increase of $ 1.0 million to the Retirement Fee (as defined in the Notes) of the High Trail Private Placement Notes to $ 3.2 million payable concurrently with redemptions of the Initial Private Placement Note. Immediately following the redemptions above, there was approximately $ 24.3 million in aggregate principal amount of the High Trail Registered Notes outstanding. High Trail Redemption Agreement 16 Table of Contents On May 23,2024, in connection with the JGB Debentures Offering, the Company entered into a redemption agreement with High Trail (the “High Trail Agreement”). Pursuant to the High Trail Agreement, the Company agreed to redeem the entire outstanding principal amount of $ 15.3 million under the High Trail Note at a redemption price of 115% for a total redemption payment of $ 17.6 million (the “Redemption Payment”). Upon High Trail’s receipt of the Redemption Payment on May 24, 2024, the High Trail Note and related Option were cancelled. In addition, the Company agreed to pay High Trail a retirement fee of $ 2.2 million and to reimburse High Trail for all of its reasonable and documented out-of-pocket expenses incurred with the release and termination of security interests relating to the High Trail Notes. The Company recognized a loss on the extinguishment of the High Trail Note of $ 1.1 million, and a gain on the extinguishment of the Purchase Option (as defined in Note 8 (Investments and Fair Value Measurements)) of $ 5.1 million, for a net gain of $ 4.0 million, which was recorded in other income (expense) on the unaudited condensed consolidated statement of operations in May 2024 upon extinguishment. As of March 31, 2025, the Company had no principal outstanding under the High Trail Notes (refer to Note 8 (Investments and Fair Value Measurements), for fair value measurements and additional discussion). In addition to redeeming $ 15.3 million and $ 27.7 million of the principal outstanding under the High Trail Notes on May 24, 2024, and March 1, 2024, respectively, for an aggregate principal redemption of $ 43.0 million at the aggregate Redemption Price of $ 49.5 million, the Holders redeemed $ 4.5 million each of principal on January 1, 2024, February 1, 2024, April 20, 2024, and May 1, 2024, for an aggregate principal redemption of $ 18.0 million at an aggregate Repayment Price of $ 20.7 million. Under the terms of the High Trail Notes, the Holders had the option to redeem a portion of the High Trail Notes not to exceed $ 4.5 million principal on the first day of each month beginning November 1, 2023, at the Repayment Price. The April 2024 payment was delayed to April 20, 2024, under the Note Amendment as discussed above. Other Income (Expense), Net The following is a summary of the charges included within other income (expense), net on the unaudited condensed consolidated statement of operations: Three Months Ended March 31, 2025 2024 Other interest expense ( 85,000 ) ( 122,000 ) Changes in estimated fair value, interest and redemption payments on High Trail Notes and convertible debentures 5,071,000 ( 1,153,000 ) Other income (expense) 94,000 ( 86,000 ) Total other income (expense) $ 5,080,000 $ ( 1,361,000 ) 17 Table of Contents 6. Stockholders’ Equity and Stock-Based Compensation Reverse Stock Split On January 24, 2025, the Company completed a reverse stock split of its outstanding shares of common stock pursuant to which every 60 shares of issued and outstanding common stock were exchanged for one share of common stock. No fractional shares were issued in the reverse stock split. Instead, the Company paid cash (without interest) equal to such fraction multiplied by $ 9.75 per share (a price equal to the average of the closing sales prices of the common stock on The Nasdaq Capital Market during regular trading hours for the five consecutive trading days immediately preceding January 27, 2025, with such average closing sales prices being adjusted to give effect to a Reverse Stock Split). All share and per share amounts included within these condensed consolidated financial statements have been retrospectively adjusted to reflect the reverse stock split. Sale of Common Stock Cowen At-the-Market Facility On March 23, 2021, the Company entered into a Sales Agreement with Cowen and Company, LLC (“Cowen”) which provides for the sale, in the Company’s sole discretion, of shares of common stock having an aggregate offering price of up to $ 350.0 million through or to Cowen, acting as sales agent or principal, which was amended on March 9, 2023 to decrease the maximum aggregate offering price to $ 200.0 million for sales made on and after the date of the amendment (the “Cowen ATM”). The Company agreed to pay Cowen a commission of up to 3.0 % of the aggregate gross proceeds from each sale of shares, reimburse legal fees and disbursements and provide Cowen with customary indemnification and contribution rights. In January 2025, the Company sold approximately 0.1 million shares of common stock under the Cowen ATM at an average share price of $ 18.94 per share, and received gross proceeds of approximately $ 1.9 million before deducting offering costs of $ 0.05 million. On February 4, 2025, the Company provided notice of its termination, effective February 14, 2025, of the Cowen ATM. Wainwright At-the-Market Facility On February 21, 2025, the Company entered into an At The Market Offering Agreement (the “ATM Agreement”) with H.C. Wainwright & Co., LLC (“Wainwright”), pursuant to which the Company may offer and sell, from time to time at its sole discretion, shares of its common stock having an aggregate offering price of up to $ 75.0 million, through or to Wainwright, acting as sales agent or principal. The Company agreed to pay Wainwright a commission of up to 3.0 % of the aggregate gross proceeds from each sale of shares, reimburse legal fees and disbursements and provide Wainwright with customary indemnification and contribution rights. In February and March 2025, the Company sold approximately 0.4 million shares of common stock under the ATM Agreement at an average share price of $ 3.84 per share, and received gross proceeds of approximately $ 1.4 million before deducting offering costs of $ 0.05 million. In April and May 2025, the Company sold approximately 0.3 million shares of common stock under the ATM Agreement at an average share price of $ 4.11 per share, and received gross proceeds of approximately $ 1.3 million before deducting offering costs of $ 0.05 million. Stock Warrants A summary of the Company’s warrant activity during the three months ended March 31, 2025 was as follows: Shares of Stock under Warrants Weighted- Average Exercise Price Weighted- Average Remaining Contractual Term Aggregate Intrinsic Value Outstanding at January 1, 2025 1,419,700 $ 91.34 1.40 $ — Granted 941,000 10.64 — — Exercised ( 280,000 ) 0.06 — — Canceled — — — — Outstanding at March 31, 2025 2,080,700 $ 67.12 0.90 $ — In connection with the registered direct offerings (as described under the heading “Registered Direct Offerings” below) the Company issued warrants to purchase shares of the Company’s common stock. 18 Table of Contents Stock Options A summary of the Company’s stock option activity during the three months ended March 31, 2025 was as follows: Shares of Stock under Stock Options Weighted- Average Exercise Price Weighted- Average Remaining Contractual Term Aggregate Intrinsic Value Outstanding at January 1, 2025 56,000 $ 937.32 7.90 $ — Granted 116,000 3.47 — Exercised — — — — Canceled ( 3,000 ) 1,016.44 — Outstanding and expected to vest at March 31, 2025 169,000 $ 290.59 9.27 $ — Vested and exercisable at March 31, 2025 30,000 $ 1,375.13 7.01 $ — For the three months ended March 31, 2025, the weighted-average grant date fair value of stock options granted was $ 3.17 per share. Stock-Based Compensation The Company recognized stock-based compensation expense for the periods presented as follows: Three Months Ended March 31, 2025 2024 Cost of product revenue $ 37,000 $ 81,000 Cost of service and other revenue — 47,000 Research and development 250,000 1,171,000 General and administrative 1,300,000 1,716,000 Total stock-based compensation expense $ 1,587,000 $ 3,015,000 The weighted-average assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants during the periods presented were as follows: Three Months Ended March 31, 2025 2024 Risk-free interest rate 4.1 % 4.0 % Expected volatility 138.5 % 80.8 % Expected term (in years) 5.7 6.1 Expected dividend yield 0.0 % 0.0 % Restricted Stock Units and Performance Stock Units The following table summarizes RSU activity during the three months ended March 31, 2025: Stock Units Weighted- Average Grant Date Fair Value per Share Outstanding at January 1, 2025 6,000 $ 272.04 Granted — — Released ( 420 ) 995.24 Forfeited ( 370 ) 193.37 Outstanding at March 31, 2025 5,210 $ 235.61 The total fair value of the RSUs that vested during the three months ended March 31, 2025 was $ 0.4 million, determined as of the date of vesting. The weighted average remaining contractual term for the RSUs is 2.8 years as of March 31, 2025. 19 Table of Contents The following table summarizes PSU activity during the three months ended March 31, 2025: Stock Units Weighted- Average Grant Date Fair Value per Share Outstanding at January 1, 2025 480 $ 2,844.00 Granted — — Released ( 480 ) 2,844.00 Forfeited — — Outstanding at March 31, 2025 — $ — During the year ended December 31, 2023, the Company reassessed the implicit service period on its performance-based stock units relative to specified revenue targets and determined that the performance conditions were met from an accounting perspective, but subject to certain certifications and approval from the Compensation Committee; therefore, the remaining expense was accelerated as of December 31, 2023. As a result of the accelerated vesting terms, the weighted average remaining contractual term for the PSUs is 0 years as of March 31, 2025. On March 14, 2025, the Compensation Committee certified that the Company had achieved the performance goals for the above PSUs. Executive Option Grants and RSUs On March 14, 2025, the compensation committee of the Company’s board of directors granted various executive officers stock options to purchase an aggregate of approximately 41,000 shares of common stock at an exercise price of $ 3.47 per share, with an effective grant date and vesting commencement date of March 14, 2025. These stock option grants were issued from the 2018 Plan. The shares subject to the stock options shall vest monthly over 48 months beginning on the one-month anniversary of their respective grant dates, such that the stock options shall be fully vested and exercisable on the four-year anniversary of their respective grant dates. Registered Direct Offerings On January 3, 2025, the Company entered into a securities purchase agreement (the “January 2025 Purchase Agreement”) with certain institutional investors, pursuant to which the Company agreed to issue and sell, in a registered direct offering priced at-the-market consistent with the rules of the Nasdaq Stock Market (the “January 2025 Offering”) (i) an aggregate of approximately 382,000 shares of the Company’s common stock, (ii) pre-funded warrants to purchase up to an aggregate of approximately 280,000 shares of common stock (the “January Pre-Funded Warrants”) and (iii) warrants to purchase up to an aggregate of approximately 661,000 shares of common stock (the “January Purchase Warrants”). Each share of common stock and each January Pre-Funded Warrant sold pursuant to the January 2025 Purchase Agreement were accompanied by a January Purchase Warrant. Both the shares of common stock and the accompanying January Purchase Warrants, and the January Pre-Funded Warrants and the accompanying January Purchase Warrants were immediately separable and were issued separately. The combined purchase price of each share of common stock and accompanying January Purchase Warrant was $ 15.120 per share. The combined purchase price of each January Pre-Funded Warrant and accompanying January Purchase Warrant was $ 15.119 (equal to the combined purchase price per share of common stock and accompanying January Purchase Warrant, minus $ 0.001 ). The gross proceeds to the Company from the January 2025 Offering were approximately $ 10.0 million (excluding up to approximately $ 10.0 million of aggregate gross proceeds that may be received in the future upon the cash exercise of the January Purchase Warrants which is contingent upon stockholder approval), before deducting placement agent fees and other offering expenses payable by the Company. Each January Purchase Warrant is exercisable for one share of common stock at an exercise price of $ 15.120 per share beginning on the effective date of stockholder approval of the issuance of the shares of common stock upon exercise of the January Purchase Warrants (the “Stockholder Approval”). The January Purchase Warrants will expire on the five-year anniversary of the Stockholder Approval. The January Pre-Funded Warrants were immediately exercisable and were exercised in full in January 2025. On January 15, 2025, the Company held a Special Meeting of Stockholders (the “2025 Special Meeting”), and obtained stockholder approval for the issuance of the shares of common stock issuable upon exercise of the Series C warrants and Series D warrants issued in a registered direct offering on October 30, 2024 pursuant to that certain securities purchase agreement and among the Company and certain institutional investors and approval, at the discretion of the Company’s board of directors, of a reverse stock split of the Company’s common stock at a ratio of between 1-for-25 and 1-for-75. On January 15, 2025, the Company’s board of directors approved a reverse stock split at a ratio of 1-for-60, and on January 24, 2025, the Company filed a certificate of amendment to effect the reverse split ratio chosen by the Company’s board of directors as further described above under the section “Reverse Stock Split.” 20 Table of Contents 7. Commitments and Contingencies The Company has entered into various operating lease agreements and a finance lease agreement, primarily relating to our office, laboratory, and manufacturing space. The future minimum payments under non-cancellable operating and finance leases as of March 31, 2025, are as follows: Operating Leases Finance Lease Remainder of 2025 $ 1,594,000 $ 255,000 2026 47,000 347,000 2027 — 355,000 2028 — 364,000 2029 — 373,000 Thereafter — 4,857,000 Total future lease payments 1,641,000 6,551,000 Less: imputed interest ( 49,000 ) ( 2,768,000 ) Total lease liabilities $ 1,592,000 $ 3,783,000 In January 2025, the Company entered into a lease termination agreement with the landlord for the facility in Pleasanton, California, that resulted in a one-time termination fee of approximately $ 0.3 million in the first quarter of 2025. The Company continued to lease the property through the end of January 2025. The Company accounted for the lease amendment as a lease termination and recorded a gain of $ 0.4 million during the three months ended March 31, 2025. Further, the restricted cash of $ 0.4 million held under the letter of credit related to the lease assumed in the acquisition of Purigen in 2022 expired concurrently with the payment of the above termination fee. Purchase Commitments The Company is currently negotiating an agreement with its instrument contract manufacturer under which it would make weekly deposits for future inventory purchases through November 21, 2025. Total payments in 2025 are expected to range from approximately $ 1.7 million to $ 2.0 million. The payments are intended to create a deposit for inventory Bionano may purchase above the 2025 minimum order quantity and guarantee the availability of certain raw materials previously purchased by the contract manufacturer to build instruments. The Company will continue to evaluate the financial impact of this commitment and assess the need for future disclosures or accruals in accordance with ASC 450. As of March 31, 2025, the Company did not accrue any amounts related to this agreement as it was not probable that the amounts would be incurred. 21 Table of Contents Restructuring The 2024 Workforce Reductions described in Note 1 (Organization and Basis of Presentation) comprised primarily of severance payments and wages for the 60-day notice period in accordance with the California Worked Adjustment and Retraining Notification (WARN) Act. There were no restructuring charges incurred for the three months ended March 31, 2025. The following is a summary of restructuring charges associated with the reduction in force for the three months ended March 31, 2024 including severance and other exit related costs: Three Months Ended March 31, 2024 Severance $ 3,874,000 Lease related expenses 211,000 Other 547,000 Total restructuring charges including in operating expenses $ 4,632,000 COGS restructuring $ 11,000 Total restructuring charges $ 4,643,000 The following restructuring liability activity was recorded in connection with the reductions in force for the three months ended March 31, 2025 included within accrued expenses on the unaudited condensed consolidated financial statements: Accrued restructuring as of January 1, 2025 $ 561,000 Restructuring charges incurred during the period — Cash payments ( 239,000 ) Accrued restructuring as of March 31, 2025 $ 322,000 Litigation From time to time, the Company may be subject to potential liabilities under various claims and legal actions that are pending or may be asserted. These matters arise in the ordinary course and conduct of the business. The Company regularly assesses contingencies to determine the degree of probability and range of possible loss for potential accrual in the unaudited condensed consolidated financial statements. An estimated loss contingency is accrued in the unaudited condensed consolidated financial statements if it is probable that a liability has been incurred and the amount of the loss can be reasonably estimated. Based on the Company’s assessment, it currently does not have any material loss exposure as it is not a defendant in any material claims or legal actions. Contingent Consideration See Note 8 (Investments and Fair Value Measurements) to the unaudited condensed consolidated financial statements for a discussion of the contingent consideration liability. 8. Investments and Fair Value Measurements The Company holds investment securities that consist of highly liquid, investment grade debt securities. The Company determines the fair value of its investment securities based upon one or more valuations reported by its investment accounting and reporting service provider. The investment service provider values the securities using a hierarchical security pricing model that relies primarily on valuations provided by an industry-recognized valuation service. Such valuations may be based on trade prices in active markets for identical assets or liabilities (Level 1 inputs) or valuation models using inputs that are observable either directly or indirectly (Level 2 inputs), such as quoted prices for similar assets or liabilities, yield curves, volatility factors, credit spreads, default rates, loss severity, current market and contractual prices for the underlying instruments or debt, and broker and dealer quotes, as well as other relevant economic measures. The following table presents the Company’s financial assets and liabilities measured at fair value on a recurring basis as of March 31, 2025 and December 31, 2024: 22 Table of Contents March 31, 2025 Total Fair Value and Carrying Value on Balance Sheet Fair Value Measurement Category Level 1 Level 2 Level 3 Assets: U.S. treasuries $ 14,606,000 — $ 14,606,000 — Money market funds classified as cash equivalents $ 2,535,000 $ 2,535,000 $ — $ — U.S. treasuries classified as restricted investments $ 11,000,000 — $ 11,000,000 — Liabilities: Convertible debentures payable $ 13,040,000 $ — $ — $ 13,040,000 December 31, 2024 Total Fair Value and Carrying Value on Balance Sheet Fair Value Measurement Category Level 1 Level 2 Level 3 Assets: U.S. treasuries $ 302,000 $ 302,000 Money market funds classified as cash equivalents $ 5,844,000 $ 5,844,000 $ — $ — U.S. treasuries classified as restricted investments $ 11,000,000 — $ 11,000,000 — Liabilities: Convertible debentures payable $ 20,362,000 $ — $ — $ 20,362,000 JGB Convertible debentures payable, High Trail convertible notes payable and purchase option liability The fair value of the JGB convertible debentures maturing in 2026, which were issued on May 24, 2024, and the High Trail convertible notes payable that were issued in October 2023, were estimated using a scenario-based analysis as of March 31, 2025 and March 31, 2024, respectively. The fair value was estimated using a lattice model. The key input assumptions utilized are summarized in the table below: Convertible Debentures Payable High Trail Convertible Notes Payable March 31, 2025 December 31, 2024 March 31, 2024 December 31, 2023 Expected volatility 97.40 % 100.00 % 82.60 % 80.20 % Risk-free interest rate 3.98 % 4.15 % 5.33 % 4.92 % Term to maturity (years) 1.08 1.33 0.42 0.80 Debt discount rate 20.10 % 19.70 % 17.10 % 17.11 % Equity discount rate 3.98 % 4.15 % 5.33 % 4.92 % The volatility is based on an analysis of the Company’s historical stock price, the risk-free rate is based on US treasury yields, the equity discount rate is based on term-specific US treasury yields, and the debt discount rate is based on the Company’s credit rating. In connection with the High Trail Notes, the purchaser was granted an option (the “Purchase Option”) which expired on the maturity date of the High Trail Notes to purchase up to an additional $ 25.0 million aggregate principal amount of private placement notes (the “Subsequently Purchased Notes”) and warrants (refer to Note 5 (Debt)). The estimated fair value of the Purchase Option as of the valuation date was assessed as the difference in the aggregate indicated value of the Subsequently Purchased Notes and the consideration to be paid upon exercising the option which was estimated to be $ 8.5 million at December 31, 2023. The outstanding amount of the High Trail Notes was redeemed on May 24, 2024, and the Purchase Option rights no longer exist. The terms used to estimate the fair value of the Subsequently Purchased Notes and warrant underlying the Purchase Option liability (the “Subsequently Purchased Warrants”) as of March 31, 2024 and December 31, 2023 are as follows: 23 Table of Contents Subsequently Purchased Notes Subsequently Purchased Warrants March 31, 2024 December 31, 2023 March 31, 2024 December 31, 2023 Expected volatility 81.50 % 80.20 % 75.80 % 66.20 % Risk-free interest rate 4.79 % 4.46 % 4.17 % 3.80 % Term to maturity (years) 1.42 1.50 5.00 5.00 Dividend yield — % — % — % — % Exercise price — — $ 3.19 $ 3.19 Debt discount rate 16.50 % 16.60 % — % — % Equity discount rate 4.79 % 4.46 % — % — % Changes in estimated fair value of convertible debentures payable in the three months ended March 31, 2025 are as follows: Convertible Debentures Payable (Level 3 Measurement) Balance as of January 1, 2025 $ 20,362,000 Change in estimated fair value, recorded in other income (expense), net ( 5,472,000 ) Conversions to common stock ( 350,000 ) Cash payments on redemptions ( 1,500,000 ) Balance as of March 31, 2025 $ 13,040,000 Changes in estimated fair value of contingent consideration liability, convertible High Trail notes payable and option liability in the three months ended March 31, 2024 is as follows: Contingent Consideration Liability (Level 3 Measurement) Convertible High Trail Notes Payable (Level 3 Measurement) Option Liability (Level 3 Measurement) Balance as of January 1, 2024 $ 10,890,000 $ 69,803,000 $ 8,534,000 Change in estimated fair value, recorded in selling, general and administrative expenses ( 640,000 ) — — Change in estimated fair value, recorded in other income (expense), net — ( 4,060,000 ) ( 3,474,000 ) Cash payments on redemptions — ( 36,663,000 ) $ — Balance as of March 31, 2024 $ 10,250,000 $ 29,080,000 $ 5,060,000 Available for Sale Investments The Company invests its excess cash in U.S. Treasury and agency securities, corporate debt securities, and commercial paper, which are classified as available-for-sale investments. These investments are carried at fair value and are included in the tables below. The Company records an allowance for credit losses when unrealized losses are due to credit-related factors. At each reporting date, the Company evaluates securities with unrealized losses to determine whether such losses, if any, are due to credit-related factors. The Company evaluates, among others, whether the Company has the intention to sell any of these investments and whether it is not more likely than not that the Company will be required to sell any of them before recovery of the amortized cost basis. Neither of these criteria were met in any period presented. The credit ratings of the securities held remain of the highest quality. Moreover, the Company continues to receive payments of interest and principal as they become due, and our expectation is that those payments will continue to be received timely. Based on this evaluation, as of March 31, 2025 and December 31, 2024, the Company determined that unrealized losses of the below securities were primarily attributable to changes in interest rates and non-credit related factors. As such, no allowances for credit losses were recorded during these periods. As of March 31, 2025 and December 31, 2024, the Company held 10 and 1 securities, respectively, which have been in an unrealized loss position for a period of less than 12 months. As of March 31, 2025 and December 31, 2024, the Company held no securities, which have been in an unrealized loss position for a period of greater than 12 months. 24 Table of Contents Realized gains and losses are calculated using the specific identification method and recorded in other income (expense) in the Company’s unaudited condensed consolidated statements of operations and comprehensive loss. The Company has the ability, if necessary, to liquidate any of its cash equivalents and marketable securities to meet its liquidity needs in the next 12 months. During the three months ended March 31, 2025, there were no sales of the Company’s available for sale securities. Amounts are reclassified out of accumulated other comprehensive income into earnings using the specific identification method when sales are realized. Interest receivable as of March 31, 2025 and December 31, 2024 was immaterial . Interest receivable is recorded as a component of prepaid expenses and other current assets on the unaudited condensed consolidated balance sheets. As of March 31, 2025, the following table summarizes the amortized cost and the unrealized gains (losses) of the available for sale securities presented within investments: Remaining Contractual Maturity (in years) Amortized Cost Unrealized Gains Unrealized Losses Aggregate Estimated Fair Value U.S. treasuries Less than 1 14,608,000 — ( 2,000 ) 14,606,000 Total maturity less than 1 year $ 14,608,000 $ — $ ( 2,000 ) $ 14,606,000 As of March 31, 2025, the following table summarizes the amortized cost and the unrealized gains (losses) of the available for sale securities presented within restricted investments: Remaining Contractual Maturity (in years) Amortized Cost Unrealized Gains Unrealized Losses Aggregate Estimated Fair Value U.S. treasuries Less than 1 11,000,000 — — 11,000,000 Total maturity less than 1 year $ 11,000,000 $ — $ — $ 11,000,000 25 Table of Contents As of December 31, 2024, the following table summarizes the amortized cost and the unrealized gains (losses) of the available for sale securities presented within investments: Remaining Contractual Maturity (in years) Amortized Cost Unrealized Gains Unrealized Losses Aggregate Estimated Fair Value U.S. treasuries Less than 1 301,000 1,100 ( 100 ) 302,000 Total maturity less than 1 year $ 301,000 $ 1,100 $ ( 100 ) $ 302,000 As of December 31, 2024, the following table summarizes the amortized cost and the unrealized gains (losses) of the available for sale securities presented within restricted investments: Remaining Contractual Maturity (in years) Amortized Cost Unrealized Gains Unrealized Losses Aggregate Estimated Fair Value U.S. treasuries Less than 1 11,000,000 — — 11,000,000 Total maturity less than 1 year $ 11,000,000 $ — $ — $ 11,000,000 As of March 31, 2025, the following table summarizes available-for-sale securities in an unrealized loss position: Less Than 12 Months 12 Months or Greater Total Fair Value Gross Unrealized Loss Fair Value Gross Unrealized Loss Fair Value Gross Unrealized Loss U.S. treasuries 14,606,000 ( 2,000 ) — — 14,606,000 ( 2,000 ) Total $ 14,606,000 $ ( 2,000 ) $ — $ — $ 14,606,000 $ ( 2,000 ) As of March 31, 2025, the available-for-sale securities listed as restricted investments in an unrealized loss position was zero . As of December 31, 2024, the following table summarizes available-for-sale securities in an unrealized loss position: Less Than 12 Months 12 Months or Greater Total Fair Value Gross Unrealized Loss Fair Value Gross Unrealized Loss Fair Value Gross Unrealized Loss U.S. treasuries $ 80,000 $ ( 100 ) $ — $ — $ 80,000 $ ( 100 ) Total $ 80,000 $ ( 100 ) $ — $ — $ 80,000 $ ( 100 ) As of December 31, 2024, the available-for-sale securities listed as restricted investments in an unrealized loss position was zero . 26 Table of Contents 9. Segment Reporting The following table presents financial information with respect to the Company’s single operating segment, including significant segment expenses, which are regularly provided to the CODM and included within consolidated operating loss: Three Months Ended March 31, 2025 2024 Revenues $ 6,457,000 $ 8,769,000 Cost of revenue 3,519,000 5,945,000 Operating expenses Salaries, wages, and benefits 5,822,000 19,820,000 Contracted services 2,679,000 5,886,000 Non-inventory materials 81,000 1,584,000 Consulting 513,000 1,863,000 Rent and facilities 572,000 1,207,000 Depreciation and amortization 1,830,000 2,398,000 Travel and entertainment 127,000 891,000 Administrative and other ( 221,000 ) 298,000 Total operating expenses 11,403,000 33,947,000 Loss from operations $ ( 8,465,000 ) $ ( 31,123,000 ) Administrative and other primarily includes operating expenses for gain on lease termination/modification, intangible assets and other long-lived assets impairment, changes in fair value of contingent consideration, disposals of property, plant, and equipment and taxes, interest, and fees. 27 Table of Contents