Plate reader software 2026
Best plate reader software for sample tracking in 2026
We compared eleven tools for microplate reader data on curve fits, plate layouts, links to sample records, audit trails, AI and price. For Prism alternatives and general analysis tools, see our lab data analysis software comparison.
Three kinds of tool
What kinds of plate reader software are there?
Plate reader software comes in three kinds. They differ most in where the results end up, and whether those results stay tied to the sample in each well.
| Kind | What it does | Where results live | Examples |
|---|---|---|---|
| LIMS and ELN platforms | Track samples and plates, store each reading on the well that holds the sample, and run the analysis there. | On the sample records. | Cypher AI, Benchling, LabKey, Scispot |
| Assay data platforms | Fit curves on data from many readers, and roll results up by compound or molecule. | In a central assay database, linked to compounds or molecules. | CDD Vault, Genedata Screener |
| Reader software | Controls its vendor's readers and fits standard curves, kinetics and dose-response on each plate. Most also install on other PCs for analysis. | In files or a database on the lab's PCs, exported to Excel or XML. | Gen5, Magellan, MARS, SkanIt, SoftMax Pro |
Most labs keep their reader software either way, since it runs the instrument. The choice is what holds the results after the read.
Why sample linkage matters
Why link plate reader results to sample records?
A reading is only useful if you know what was in the well. Reader software keeps the plate layout in its own file, so the link to stocks, constructs or donors usually lives in a spreadsheet beside the export. Here are four common signs that link is slipping, and what changes in Cypher AI.
- The plate map is a spreadsheet next to the export.In Cypher AI, the plate map is part of the plate record, so each well already knows its sample.
- Nobody can say which stock went into well E6.In Cypher AI, lineage runs from the stock to the plate to the reading.
- Results get pasted into a sheet by hand.In Cypher AI, readings upload onto the right wells, matched by sample ID or by plate barcode and well.
- Each new plate rebuilds last week's analysis.In Cypher AI, an analysis saved as a widget runs the same way on the next plate with the same layout and export format.
At a glance
How do these tools analyze plates and link results to samples?
| Tool | Kind | Analysis | Plate layouts | Link to sample records |
|---|---|---|---|---|
| Cypher AI | LIMS and ELN platform | The agent writes the fit you describe, such as a 4PL dose-response, and saves it as a widget | Plate maps from 6 to 384 wells | Native sample records, with lineage. Each reading is stored on the sample in its well. Any reader's CSV export; the agent builds parsers for other formats |
| Benchling | R&D platform with ELN, Registry and Inventory | Curve fits, charts and statistics in the ELN entry, through Benchling Automation | Plates in Inventory; plate-based workflows in Automation | Native sample records, with lineage. Automation links results to the samples that produced them. 200+ instrument connectors, including plate readers |
| LabKey LIMS | LIMS with an ELN | Transformation scripts on import; reports and charts | Plates and plate sets in LIMS Enterprise and Biologics LIMS | Native sample records, with lineage. Each assay design maps results to a sample. Import scripts take any instrument format |
| Scispot | ELN, LIMS and data integration platform | Smart Actions parse plate files and apply QC rules | Plate maps for 96- and 384-well plates | Native sample records. Smart Actions map wells to sample IDs through the plate manifest. 350+ instrument types |
| CDD Vault | Assay data platform for drug discovery | Dose-response, enzyme kinetics and binding fits, normalized to plate controls | Control layouts for 96-, 384- and 1536-well plates | Compound or molecule records. Results attach to registered molecules and batches through compound plate maps. Any reader's export |
| Genedata Screener | Enterprise screening data platform | Automated curve fitting, model selection and QC across screening, high-content, SPR and BLI assays | Set centrally in each assay workflow | Compound or molecule records. Results are reported per molecule; sample records connect through APIs to an ELN or LIMS |
| Gen5 (Agilent BioTek) | Software for Agilent BioTek readers | 4- and 5-parameter fits, EC50 and IC50, Z', kinetics and spectral scans | Predefined plate types and 150+ quick-start protocols | Plate file only. Sample IDs sit in the experiment file; one-button export to Excel |
| Magellan (Tecan) | Software for Tecan readers | ELISA standard curves, including 4- and 5-parameter and LogitLog fits; ICx; enzyme kinetics | Plate definition editor; formats up to 1536 wells | Plate file only. Sample ID lists import into the plate; exports Excel, ASCII and XML for a LIMS |
| MARS (BMG LABTECH) | Software for BMG LABTECH readers | 4- and 5-parameter fits, EC50 with confidence intervals, enzyme kinetics, parallel-line analysis, Z' | 30+ predefined assay protocols, with linked analysis templates | Plate file only. Exports Excel and ASCII; ActiveX, DDE and SiLA interfaces for a LIMS |
| SkanIt (Thermo Fisher) | Software for Thermo Scientific readers | Linear and logistic fits, parallel-line analysis, Km and Vmax, Z-factor | Virtual Pipetting Tool for plate layouts | Plate file only. Sample information is set in the plate layout; exports .xlsx, .pdf, .xml and .txt |
| SoftMax Pro (Molecular Devices) | Software for Molecular Devices readers | 21 curve fit options for ELISA, quantitation, potency and kinetic assays | 170+ ready-to-run protocols you can customize | Plate file only. Sample names sit in the plate template; XML export feeds a LIMS or SDMS |
Native sample records: each result sits on a tracked sample. Compound or molecule records: results attach to registered compounds or molecules, not to physical samples. Plate file only: sample names live in the reader's file, and linking them to sample records needs a separate LIMS.
AI, records and price
How do they compare on AI, audit trails, data handling and price?
| Tool | AI | Audit trail and GxP option | Where your data lives | Published price |
|---|---|---|---|---|
| Cypher AI | One agent across the ELN, LIMS and analysis; you approve its plan before records change | Part 11-style audit trails: field-level history on LIMS records, e-signature workflows in the ELN. Built for R&D, not validated GxP | Cloud, SOC 2 Type II; admins choose the AI models. Enterprise is single-tenant, in your own cloud account in the US, the EU or mainland China | Free $0, with 15 AI messages a month; Pro $100 per user a month, with the LIMS |
| Benchling | Benchling AI; selected capabilities use monthly credits that expire | Validated Cloud: a dedicated, validated tenant with Part 11 e-signature controls | Cloud; GxP work in a dedicated tenant | Quote only |
| LabKey LIMS | LabKey AI answers plain-language questions on lab data, in a first phase | Time-stamped history of every sample, action and user; validation is an add-on | LabKey's cloud; on-premise for Biologics LIMS | $34,080 a year with 10 users; plates need LIMS Enterprise, $53,520 |
| Scispot | Plato plate agent; AI file processing, reviewed before results are saved | Audit-Ready plan adds e-signatures, approvals, audit trails and validation support | AWS, US by default, EU on request; SOC 2 Type II | Custom annual pricing, unlimited users |
| CDD Vault | AI module for similarity search, bioisosteres and docking; Claude connector in early release | Audit trail and support for Part 11 and GxP workflows in every subscription, per CDD | Hosted by CDD; Enterprise adds a single-tenant instance | Quote only; free visualization tool and 30-day trial |
| Genedata Screener | No assistant found; Genedata describes its data as AI-ready | GxP support with immutable records and audit logs | Cloud-based access, with several deployment options | Quote only |
| Gen5 | None found | Gen5 Secure: permissions, e-signatures and audit trails, with a validation package | Gen5 files on each PC where it's installed; it controls the reader from one PC and also analyzes on PCs not connected to it | Not published; comes with the reader, no recurring fees |
| Magellan | None found | Magellan Tracker: user administration, audit trails and e-signatures | On the PC where it's installed | Not published |
| MARS | None found | BMG LABTECH says the software is designed to comply with 21 CFR Part 11 | On any PC you install it on | Included with every BMG LABTECH reader, on unlimited PCs |
| SkanIt | None found | Drug Discovery Edition: Windows sign-in, audit trails and digital signatures | Research Edition saves files to local, network or cloud drives; Drug Discovery Edition uses a database | Research Edition: royalty-free license, unlimited installs; Drug Discovery Edition: quote only |
| SoftMax Pro | None found | GLP Mode adds audit trails and e-signatures; GxP Software adds document workflows and validation services | On Windows PCs; GxP Software adds a database | Standard $2,418 a year for one license |
The list
Which plate reader software should you consider?
Cypher AI
Our productCypher AI is an ELN, LIMS and analysis platform with one AI agent that works across all three.
- Best for
- R&D assay teams and core labs that run the same assays every week and need each result tied to the sample behind it. Start with the plates you use today, and add a field when an assay needs it.
- Results and samples
- Upload the reader's CSV export, and each reading lands on the sample in its well, matched by sample ID or by plate barcode and well. For other export formats, the agent builds a parser once. Kinetic reads keep their time points, and each result traces back to its source stock. The File Agent can send each finished run from the reader's PC.
- AI
- Ask the agent for the analysis you run, such as a 4PL fit that flags outlier wells. It writes and runs the Python, and you can save it as a widget that reruns on later plates with the same layout and export format, by hand or when a new file arrives. You approve the agent's plan before records change.
- Pricing
- Free is $0, with 15 AI messages a month and one private analysis. Pro is $100 per user a month and adds the LIMS, team features and expanded AI usage. Ten Pro seats come to $12,000 a year; LabKey LIMS, the other platform here that publishes a price, is $34,080 a year for 10 users. Eligible startups get 90 days of Pro free. See the pricing page.
- Look elsewhere if
- you need a validated GxP system today, or software that controls the reader. Cypher AI works from your reader's exports.
Working with the teamWork directly with the people building Cypher AI as you set up your plate workflows. Every new account can book a free onboarding call.
Benchling
Benchling is a cloud R&D platform with an ELN, Registry and Inventory. Benchling Automation brings instrument data into the same record.
- Best for
- R&D groups already on Benchling that want plate reader data next to their registry.
- Results and samples
- Automation lists 200+ instrument connectors, including plate readers. Results link to the samples that produced them, and new plate-based workflows were announced on October 15, 2026.
- AI
- Benchling AI. Selected capabilities use monthly credits that expire.
- Pricing
- Quote only. Validated Cloud is a dedicated tenant for GxP work.
- Look elsewhere if
- you want a published price or a self-serve start.
LabKey LIMS
LabKey LIMS is a LIMS with an integrated ELN and an assay framework that ties every result to a sample.
- Best for
- Labs that want sample tracking and assay data together at a published price, with LabKey's team setting it up.
- Results and samples
- Import scripts transform instrument files on the way in. Plates and plate sets come with LIMS Enterprise and Biologics LIMS.
- AI
- LabKey AI, launched July 29, 2026, answers plain-language questions on lab data. LabKey calls it a first phase.
- Pricing
- LIMS is $34,080 a year with 10 users, and LIMS Enterprise is $53,520. Hosting, implementation and training are included.
- Look elsewhere if
- you want plates on the entry tier, or a lower price for a few users.
Scispot
Scispot is a lab platform with an ELN, LIMS and data integration, sold with forward-deployed scientists and engineers who set it up around an agreed outcome.
- Best for
- Labs that want a vendor team to connect instruments and build workflows for them.
- Results and samples
- Smart Actions parse plate reader files, map wells to sample IDs and apply QC rules. You review the result before it's saved.
- AI
- Plato, Scispot's plate agent, suggests layouts and charts. Smart Actions use AI to reshape files.
- Pricing
- Custom annual pricing with unlimited users. No dollar figures are published.
- Look elsewhere if
- you want to start on your own, without a scoped project.
CDD Vault
CDD Vault is a drug discovery data platform that registers compounds and stores assay results against them.
- Best for
- Small-molecule teams tracking dose-response and SAR across compounds and CRO partners.
- Results and samples
- Import plate data with a compound plate map, normalize to control wells and fit curves. Results attach to registered molecules and batches.
- AI
- An AI module for similarity search, bioisosteres and Boltz-2 docking, and a Claude connector in early release since July 8, 2026.
- Pricing
- Quote only. Freemium is a free visualization tool, and the full platform has a 30-day trial.
- Look elsewhere if
- your work isn't organized around compounds and batches.
Genedata Screener
Genedata Screener is an enterprise platform for analyzing screening assay data, from high-throughput screens to high-content, SPR and BLI assays. Genedata has been part of Danaher since 2024.
- Best for
- Pharma and large biotech screening groups with an informatics team to configure workflows.
- Results and samples
- Automated curve fitting, model selection and QC, with results reported per molecule and sent to ELNs and LIMS through APIs.
- Pricing
- Quote only.
- Look elsewhere if
- you're a startup or academic lab running a few plate assays a week.
Gen5 (Agilent BioTek)
Gen5 controls Agilent BioTek plate readers, from endpoint and kinetic reads to spectral and well-area scans, and analyzes the data. It also installs on PCs not connected to a reader for analysis, and imports raw-data text files from other sources.
- Best for
- Labs with Agilent BioTek readers that want each plate analyzed in the software that read it.
- Pricing
- Not published. Gen5 comes with the reader, and Agilent lists no recurring fees. Gen5 Secure adds permissions, electronic signatures and audit trails, with a validation package.
- Look elsewhere if
- you need a central sample registry and lineage across assays.
Magellan (Tecan)
Magellan is Tecan's reader control and data analysis software, with full ELISA and EIA standard curve analysis.
- Best for
- ELISA and EIA labs on Tecan readers.
- Pricing
- Not published. Magellan Tracker adds user administration, audit trails and electronic signatures.
- Look elsewhere if
- you run readers from more than one vendor.
MARS (BMG LABTECH)
MARS is BMG LABTECH's data analysis software. It works alongside the Reader Control software that runs BMG readers, and a template linked to a read protocol analyzes a plate in two clicks.
- Best for
- Labs with BMG LABTECH readers that want broad curve fitting at no extra cost.
- Pricing
- Included with every BMG LABTECH reader, on as many computers as you need.
- Look elsewhere if
- you need results kept with sample records, or data from other vendors' readers.
SkanIt (Thermo Fisher)
SkanIt is Thermo Fisher's software for its Thermo Scientific microplate readers, including Varioskan, Multiskan and Fluoroskan.
- Best for
- Labs with Thermo Scientific readers.
- Pricing
- The Research Edition comes with a royalty-free license for unlimited installs, downloaded after you verify a Thermo Scientific reader purchase. The Drug Discovery Edition, which adds Windows sign-in, audit trails and digital signatures, is a separate catalog item priced by quote.
- Look elsewhere if
- you want one place for results across vendors, or across plates over time.
SoftMax Pro (Molecular Devices)
SoftMax Pro is Molecular Devices' software for acquiring, analyzing and reporting microplate data, from research to regulated QC.
- Best for
- Labs on Molecular Devices readers.
- Pricing
- Standard is $2,418 a year for one license in Molecular Devices' US store. GLP Mode adds audit trails and electronic signatures, and GxP Software adds document workflows and validation services.
- Look elsewhere if
- you want results kept with sample records rather than in plate files.
How to choose
Which plate reader software fits your team?
Most R&D assay teams and core labs should start with Cypher AI. A few narrower needs point elsewhere.
| Your team | Start with | Why |
|---|---|---|
| Assay development at a small biotech | Cypher AI | Readings land on tracked samples, and an analysis built on one plate reruns on later plates of the same assay. The Startup Program gives 90 days of Pro free. |
| Core facility running assays for several groups | Cypher AI | Each group's readings stay linked to its samples, while shared assay widgets standardize analysis across repeat runs of the same assay and export layout. Ask us about core lab pricing. |
| Protein, enzyme or cell-based screening across many plates | Cypher AI | Endpoint and kinetic reads upload onto wells and trace back to the source stock or construct. |
| Academic lab with one reader | Your reader's software, then Cypher AI's Academic Program | It came with the reader and fits each plate. Add Cypher AI when results need to stay with samples across plates. |
| Regulated QC or GLP lab | Your reader's compliance edition, such as SoftMax Pro GxP or Gen5 Secure | Built for Part 11 work, with audit trails, electronic signatures and validation support. |
| Industrial high-throughput screening group | Genedata Screener | Built for screening volumes across many assay technologies, with an informatics team to run it. |
| Medicinal chemistry team tracking SAR | CDD Vault | Dose-response results attach to registered compounds and batches, next to SAR tools. |
FAQ
Questions about plate reader software
What software do I need to analyze ELISA plate reader data?
Your reader's software fits ELISA standard curves on each plate. Gen5, MARS and Magellan list 4- and 5-parameter fits, and SoftMax Pro lists 21 curve fit options. To keep each concentration with its sample, upload the reading to a LIMS such as Cypher AI, where the agent fits the curve and saves the analysis to rerun on later plates of the same assay.
How do I link plate reader results to sample IDs?
Give each well a sample before the read, then match the export to it. Reader software keeps sample names in its own plate layout. A LIMS records which sample sits in each well, so an upload matched by plate barcode and well puts each reading on the right sample. In Cypher AI, that match happens on upload.
Can I analyze data from another vendor's plate reader?
Reader software controls only its own vendor's readers, but several programs analyze imported data: Gen5 imports raw-data text files, Magellan imports raw data and CSV or text files, and SoftMax Pro sells importer add-ons. Reader-neutral tools such as Cypher AI, CDD Vault and Genedata Screener take exports from any reader and keep them in one place, which helps when a lab or core runs several brands.
Is there free plate reader software?
Reader software usually comes with the reader. BMG LABTECH includes MARS with every reader on unlimited PCs, and SkanIt's Research Edition has a royalty-free license for unlimited installs. Cypher AI's Free plan is $0, with 15 AI messages a month and one private analysis; readings on wells come with Pro, at $100 per user a month. CDD Vault offers a free visualization tool.
Do I need a 21 CFR Part 11 edition of my plate reader software?
Only if the data supports regulated work, such as GLP studies or QC release. Molecular Devices, Agilent, Thermo Fisher and Tecan each sell an edition with audit trails and electronic signatures. Cypher AI has Part 11-style audit trails and e-signature workflows for R&D, but it isn't a validated system.
Why aren't Prism, Excel or BI tools on this list?
They analyze numbers well but don't run readers or track samples. GraphPad Prism and Excel are common after an export, and Tableau or Power BI suit dashboards across many results. For analysis tools, see our lab data analysis software comparison.
First steps
How do you try Cypher AI with your plate reader data?
- Create a free account.Start on the free plan, with no card.
- Upload an export and try an analysis.Add a plate reader export to an analysis and ask the agent for the fit you run. Free includes one private analysis.
- Turn on Pro, or apply to the Startup Program.Pro links readings to tracked samples and wells in the LIMS. Eligible startups get the first 90 days free.
For larger R&D teams, Enterprise runs as a single-tenant cloud deployment in your own cloud account, with a forward-deployed engineer who helps set up plate workflows and data integrations.
How we picked
How did we choose and check these tools?
Cypher AI is our product, so it's listed first. The others are grouped by kind, then alphabetical: LIMS and ELN platforms, assay data platforms, then the software from five plate reader makers.
Features and prices come from each vendor's own pages, and where a vendor only quotes, we say so. This compares published information, not hands-on tests.
Sources
Vendor details checked on October 23, 2026, on each vendor's own pages. Spotted something out of date? Tell us at cypherbio.ai/contact and we'll fix it.
- Benchling: Automation, Inventory, AI credits, Validated Cloud, pricing, Benchtalk 2026 launches (October 15, 2026)
- LabKey: pricing, LIMS, assay and plate management, assay designs, LabKey AI (July 29, 2026)
- Scispot: pricing, Smart Actions, Plato, security and compliance
- CDD Vault: pricing, curve analytics, plate data import, AI module, Claude connector (July 8, 2026)
- Genedata: Screener, Danaher acquisition (August 19, 2024)
- Agilent BioTek: Gen5
- Tecan: Magellan, Standard and Tracker
- BMG LABTECH: microplate reader software
- Thermo Fisher: SkanIt, editions
- Molecular Devices: SoftMax Pro, SoftMax Pro GxP, online store
- Cypher AI: data analysis, LIMS, pricing, Startup Program · Security: trust.cypherbio.ai
Product names are trademarks of their owners. Cypher AI isn't affiliated with or endorsed by any other company on this page.