Data Analysis · Plate readers
Cypher AI Data Analysis for plate reader assays
Turn your plate reader export into a reusable analysis. Review the well mapping and the analysis once, then rerun the saved analysis on later plates that use the same assay setup.
Free plan, no card. Putting readings on plates and samples uses the LIMS, which comes with Pro and Enterprise.
The problem
Why does routine plate reader analysis take so long?
Because the math, the plate layout and the samples often live in different places, such as a spreadsheet template, an ELN entry and another sheet. So every new plate means copying values in, pointing formulas at the control wells and pasting results into slides. By then a number no longer points back to its sample.
In Cypher AI, the readings land on the plate in the LIMS, the analysis is a widget the whole team runs, and each result traces back to its well and sample.
How it worksAI-assisted
How does Cypher AI analyze plate reader data?
Set up the plate, export from the reader as you do today and check the import. Then the agent writes and runs the analysis you describe.
Reader export
viability_plate8.xlsx- Exported from the reader's own software
- Header rows, then a 96-well grid of luminescence values
LIMS · Plate 8, set up first
96 readings on 96 wellsThe plate's samples, doses and units are in the LIMS before the upload. Columns 1 and 12 hold the DMSO and no-cell controls. Each reading lands on its well and sample.
Example widget · Viability 4PL fit
Dose-response fits, IC50 estimates and fit-quality flags- Normalized to the DMSO and no-cell wells
- IC50s with 95% CIs where they can be estimated, and inconclusive fits flagged
- The chart updated on the team's dashboard
- Set up the plateCreate or select the LIMS plate and confirm its sample and control layout. For dose-response, supply the concentrations and units. Start with the fields you use today.
- Put the readings on the plateYour reader's software still runs the instrument. Export the results, then choose Add Data on the plate and pick the parser the agent wrote for your file layout. Review the preview before saving.
- Describe the analysisAsk in plain words. The agent writes the Python, runs it and names the controls it normalized to.
- Save it as a widgetLater plates with the same assay setup are a short form and a Run button. If the export format or the assay changes, update the parser or the widget.
Assays
Which plate reader assays can Cypher AI analyze?
The routine ones most labs run every week. These are examples of what you can ask for. The agent writes each one in Python you can read and edit.
| Assay | Typical read | What you ask the agent for |
|---|---|---|
| ELISA | Absorbance at 450 nm | Fit a 4-parameter logistic to the standards, back-calculate the samples and flag replicate CVs above 15%. |
| Cell viability and dose-response | Luminescence or fluorescence, over a concentration series | Normalize to the vehicle and no-cell wells, fit a 4-parameter logistic per compound, report relative IC50s with 95% CIs where they can be estimated, and flag inconclusive fits. |
| Growth curves | OD600 over time, often with fluorescence | Subtract the blank, then report lag time, maximum growth rate and fluorescence per OD. |
| Enzyme kinetics | Absorbance or fluorescence over time, across a substrate concentration series | Estimate initial rates from the linear portion of each progress curve, then fit rate versus substrate concentration to Michaelis-Menten to estimate Km and Vmax. |
| Protein quantification | BCA at 562 nm, Bradford at 595 nm | Fit the BSA standard curve and report each sample's concentration in mg/mL. |
| Screening plates | Any endpoint read | Calculate Z′ for each plate and call hits more than three standard deviations from the negative controls. |
Kinetic reads keep a timepoint on every reading. For enzyme kinetics, the agent also has built-in guidance on matching the model to the experiment.
Linked to samplesCore
How do plate reader results stay linked to samples?
The readings are stored on the plate in the LIMS, not left in a file, so each one sits on its well and the sample in it.
- Each reading knows its sample. A sample's page lists its readings next to its lineage, back to the stock it came from.
- Each upload is a step in a workflow. It records who uploaded it and when. The instrument name and serial number come from what you enter in the upload form, not from the export. A plain CSV stays on the step, and a parser keeps the file it read in its Run History.
- Results go where decisions are made. Save an analysis's outputs to the ELN entry and its charts to a dashboard. A Marketplace order records the samples it started from.
WidgetsCore
How do you rerun the same analysis on the next plate?
Save the analysis as a widget. Anyone you share it with runs it from a form, with the same code underneath every time.
- One click on the next plate. Enter the plate's ID and click Run, with the author's defaults filled in.
- Or let a new file start it. Set up a File Action, and each export that lands in a chosen project folder runs the widget on that file. The run gets the file, not a plate ID, so it analyzes the file. A parser can import readings this way only when it knows which LIMS plate the file belongs to. Otherwise the import stops instead of guessing.
- The same code every run. Each edit is a new version, and Run History shows who ran which one.
- The dashboard keeps up. Connect the widget to a team dashboard, and each run replaces its chart with the new one.
Plate reader files
Which plate reader files can Cypher AI read?
Cypher AI can parse CSV, tab-delimited text and .xlsx plate reader exports using a parser tailored to your file layout. SoftMax Pro, Gen5 and MARS, for example, can all export to Excel.
| What's in the export | How the parser handles it |
|---|---|
| Run settings above the data | Skips the header rows and reads the values below. |
| A plate grid, 8 × 12 or 16 × 24 | Turns the grid into one reading per well. |
| One row per well | Reads each row as it is. |
| Several plates in one file, or one sheet per plate | You match each one to its plate in the LIMS before anything is saved. |
| Kinetic reads | Keeps the timepoint on every reading. |
| An older .xls workbook | Save it as .xlsx first. |
You review every import before it's saved. The agent test-runs the parser on your example file, and Add Data shows a preview of what will land on each well. A file with rows that can't be placed is refused whole, not half imported. Create and test a parser for each new export layout.
Get started
How do you start analyzing plate reader data in Cypher AI?
First steps
- Try it on one exportCreate a free account, upload an export to a new analysis and ask the agent for the fit you run every week.
- Put readings on your platesTurn on Pro for the team to get the LIMS, with AI included. Startups can apply to the Startup Program for 90 days free.
- Get a walkthroughBook a free onboarding call, or follow the in-app lesson on uploading instrument data. You talk directly to the people who build Cypher AI.
Academic lab? See the Academic Program. Need it in your own cloud account? Cypher AI Enterprise is a single-tenant cloud deployment with a forward-deployed engineer.
FAQ
Questions about plate reader analysis in Cypher AI.
What is the best software for plate reader data analysis?
For routine assays whose results need to stay linked to samples, Cypher AI: the readings land on the plate in its LIMS, and the analysis is a widget that reruns on later plates of the same assay. Your reader's own software stays in place for running the reads. Our comparison of plate reader software covers the other options.
Can Cypher AI connect directly to my plate reader?
Cypher AI works from the reader's export, not a live connection to the instrument. To skip manual uploads, the Cypher AI File Agent on the reader's PC copies each new export into a project folder, where a widget can pick it up.
How do I fit a dose-response curve to plate reader data?
Start from a LIMS plate whose wells carry each compound, its concentration and units, and the control wells, and upload the export onto it. Then ask the agent in plain words, for example “normalize to the DMSO and no-cell wells, fit a 4-parameter logistic per compound, report relative IC50s with 95% CIs where they can be estimated, and flag inconclusive fits”. Say whether your assay needs a relative IC50 or the concentration that gives 50% inhibition against the controls. The agent returns the estimates, the plots and the code it ran.
Does the agent change LIMS records without asking?
Not in Ask mode, the default. When the agent uploads readings to a plate, it shows the file, the plate and the workflow on a Confirm plan card and waits for your approval. Each person can switch their agent to Auto, which applies LIMS changes straight away. A File Action you set up is different: it runs on each new file without asking.
Which plate formats does Cypher AI support?
Plates of 6 to 384 wells, including the common 96- and 384-well formats. Readings can be endpoint or kinetic, and each reading can carry a unit and a timepoint.
Can I use Cypher AI for GxP or 21 CFR Part 11 work?
Cypher AI is built for R&D. It has Part 11-style audit trails and e-signature workflows and SOC 2 Type II controls, but it isn't a validated GxP system. For validated release testing, keep your validated reader software.
How much does plate reader analysis in Cypher AI cost?
Analysis is on every plan. Free includes 15 AI messages a month and one private widget. Readings on plates need the LIMS, which comes with Pro at $100 per user a month and with Enterprise, from $25K per year.
Sources: export options on the SoftMax Pro, Gen5 and MARS product pages, checked October 23, 2026; security controls in the Cypher Trust Portal. Spotted something out of date? Tell us.