Laboratory Information Management System
Cypher AI LIMS
Samples, containers, and workflows with full lineage tracking. Flexible enough for real biology.
The LIMS is part of Pro and Enterprise and works inside a team.
Assay plate 7
CTR-20260922-0005content_copySPL-20260915-0034
content_copyMichael Taylor changed Quantity (Volume) from 200 µL to 180 µL
6 hrSep 22, 2026, 09:40 AMPlate 7 viability screen
WFL-20260922-0003content_copySTP-20260922-001288 reqSTP-20260922-001396 reqSTP-20260922-001496 req8×1296 paintedTip: drag Add Step onto a container or material to build a step from it
Assay plate 7
CTR-20260922-0005content_copyUpload measurements
sampleId (or containerId + well); other columns are measurement tags like OD600 (AU). Use Download example for the wide, long, and by-location templates.96 data points across 96 samples
Luminescence: 96STP-20260922-0014
content_copymore_vertNo timepoint
E6 · SPL-20260922-0148 — Luminescence: 10622 RLU
1s1sA 1:10 dilution: 50 µL of the 10 mM stock into 450 µL DMSO. The stock tube drops from 180 µL to 130 µL.
CTR-20260915-0021 (decremented)50 µL500 µL1 mMCPD-13 1 mM (tube)2sDone. CPD-13 1 mM is in a new tube, CTR-20260922-0031, holding 500 µL. CTR-20260915-0021 now holds 130 µL, and the new tube is linked to it in the workflow lineage.
What you get
What Cypher AI LIMS gives you.
Cypher AI LIMS keeps sample data and experimental data in sync, from the stock tube to the plate reading.
The problem
Where sample tracking breaks down today.
Traditional LIMS make you bend your science to fit their schema, and every change becomes an IT project.
See it workCore
Plan the plate, record the transfer, load the readings.
Three everyday jobs on plate 7, done by hand in the app. Each tab is one of them.
Plate Map
Applying to 1 plate · 8×12CTR-20260922-0005Select a value, then click wells to paint · row/column header or corner fills (click again to clear) · shift-click to fill a range
Darker wells already hold a sample. Whether painting an empty well also creates a blank sample is set per key in the legend (“Create blank samples for empty wells”).
Add Step
Plate 7 viability screen
WFL-20260922-0003content_copySTP-20260922-001288 reqAssay plate 7Assay plate 7
CTR-20260922-0005content_copyUpload measurements
sampleId (or containerId + well); other columns are measurement tags like OD600 (AU). Use Download example for the wide, long, and by-location templates.96 data points across 96 samples
Luminescence: 96STP-20260922-0014
content_copymore_vertNo timepoint
E6 · SPL-20260922-0148 — Luminescence: 10622 RLU
- Each step keeps its inputs, outputs and volumes
- The source is drawn down by what you transfer
- Readings attach to the sample in each well
Workflow
A sample's life in Cypher.
The same path as the tabs above, from registration to readings.
- RegisterCreate samples and give each one a place: a well, a tube or a box.
- ProcessPlan the plate, record transfers and load readings as workflow steps.
- TraceFollow any well back to the stock it came from.
- ConnectUse the same records in ELN entries and analyses.
Samples, materials, containersCore
Each sample records what it is, how much is left, and where it is.
A material is what a thing is. A sample is an amount of it. A container is where that amount sits. Below is the 10 mM stock of CPD-13 that plate 7 was made from.
SPL-20260915-0034
content_copyMichael Taylor changed Quantity (Volume) from 200 µL to 180 µL
6 hrSep 22, 2026, 09:40 AM- Gets an ID.Assigned on the first save, like SPL-20260915-0034.
- Location.Its container and position, like E6 on a plate. The container carries the barcode and storage path.
- How much is left.Steps that use the sample deduct from its volume automatically. You can also adjust it by hand.
- Lot and expiry.The metadata card starts with lot_number and expiration_date. Add any other key you track.
- What it contains.Each row points to a material in the registry, with its share of the volume.
- Every change, with a name and a time.The 20 µL draw-down was written by the Dilution step and logged under the person who recorded it.
Easy access to where each container is stored.
Tubes, plates, racks and boxes sit inside storage locations you name: a room, a freezer, a shelf. The container page shows the full path and every step that used it.
CPD-13 10 mM
CTR-20260915-0021content_copyDilutionSTP-20260922-0011
Sample RegistrationSTP-20260915-0006
Every stock of a material, in one list.
One record per compound, cell line, plasmid or reagent, with its type and subtype. Its page lists every stock container with lot, expiry and what is left, and shows expired lots in red.
CPD-13
CHM-20260908-0003content_copyWhat a container can be
- Plates6- to 384-well, or a custom grid
- Racks and boxes4 × 6 tube racks, 9 × 9 boxes
- Single vesselsTubes, cryovials, flasks, bottles
- StorageRooms, freezers and shelves that hold other containers
The inventory and the experiment read the same records.
Workflows and lineageCore
Lineage is recorded as the work is logged.
Every step you log links what went in to what came out, so you can trace any sample from start to finish.
Plate 7 viability screen
WFL-20260922-0003content_copySTP-20260922-001288 reqSTP-20260922-001396 reqSTP-20260922-001496 req8×1296 paintedTip: drag Add Step onto a container or material to build a step from it
- Lanes keep the work apart.The compound plate and the cells sit in separate lanes until they meet on the assay plate.
- Steps with a work type.Each has its own ID and request count, and its border shows its status. Green means completed.
- Containers you can open.Hover a plate to see which wells are filled. Click it to go to the plate.
- The plate map.The painted layout hangs off the plate it describes. Click it to edit and apply again.
- Readings in the same graph.An upload is a Measurement step on the plate, next to the work that produced it.
- Easily build from the canvas.Drag Add Step onto a container to start a step with it as the input. Transformation and Purify DNA are built-in protocol steps.
Data integrity
Every change is logged.
Samples, containers, materials and steps keep a field-level history, and deleted records stay recoverable.
Michael Taylor changed Status (cascaded to 96 sample(s)) from active to disposed
1 hrSep 22, 2026, 04:31 PMMichael Taylor changed Storage Location from (empty) to Incubator 2 (37 °C)
6 hrSep 22, 2026, 10:05 AMJamie Cho changed Name from Assay plate 7b to Assay plate 7
7 hrSep 22, 2026, 09:21 AMRemove measurement step?
This will remove STP-20260922-0014 and hide its measurement data from list views. The step + data points are soft-deleted — they can be restored later.
Every well traces back to its source.
IDs and labelsCore
Every record gets an ID. Every container can carry a label.
- The ID is assigned for you.Each sample, container, material, step and workflow gets one when it is created: a type prefix, the date and a counter, like CTR-20260915-0021.
SPLCTRDNARNAPRTCELRGTCHMSTPWFL - Print a label for the tube, box or plate.From the container's page, print a QR label with its ID and name. The code on the label is the container's ID, so the label and the record match.
A team admin turns label printing on, with nothing to install.
CPD-13 10 mM
CTR-20260915-0021content_copyDymo 3/4" × 2.5" label, as rendered for printing
With the agentAI-assisted
Describe the work, check the plan, approve it.
The agent reads the LIMS freely. Anything it would change shows up first as a Confirm plan card, with the source it will draw down and any warnings.
1s1sA 1:10 dilution: 50 µL of the 10 mM stock into 450 µL DMSO. The stock tube drops from 180 µL to 130 µL.
CTR-20260915-0021 (decremented)50 µL500 µL1 mMCPD-13 1 mM (tube)2sDone. CPD-13 1 mM is in a new tube, CTR-20260922-0031, holding 500 µL. CTR-20260915-0021 now holds 130 µL, and the new tube is linked to it in the workflow lineage.
1s1sThe preview matched all 96 wells to their samples. Review the plan below, then Approve.
CTR-20260922-0005CSV file "ctg_plate7.csv"CellTiter-Glo, plate 7EnVisionWFL-20260922-00033sDone. The 96 luminescence readings are on the plate's samples as step STP-20260922-0014. The no-cell wells in column 12 read 450–514 RLU, and the DMSO wells in column 1 average 52,100 RLU.
1sYou have 365 µL of CPD-13 10 mM across three tubes:
| Tube | Left | Stored in |
|---|---|---|
| CTR-20260915-0021 | 130 µL | Shelf 3 |
| CTR-20260915-0022 | 200 µL | Shelf 3 |
| CTR-20250611-0014 | 35 µL | Freezer 2 (−20 °C) |
All three are listed as sources you can draw from. The two on Shelf 3 were made this week.
LIMS writes wait for your approval. Switch a chat to Auto and they apply as you go.
Reading never asks: stock, locations, lineage and readings come back straight away.
- Turn a notebook entry into samples and containers
- Bring in samples from a spreadsheet, plate layouts included
- Restore a sample that was deleted by mistake
- Fill in a new sample's metadata from its description
Connected
Connected to your ELN and analyses.
Two ways in
Start with your team, or bring the whole lab.
Turn on Pro when the team needs a LIMS.
- The LIMS comes with Pro, $50 per user a month
- It works inside a team, so the people who share a freezer share the records
- Try Demo Data fills it with an example you can remove
Your own deployment, set up with you.
- A dedicated deployment in your cloud account
- Data residency, SSO and custom data integrations
- A forward-deployed engineer and priority support
First steps
- Create a teamSign up for Pro and create a team for your lab. No schema design needed up front.
- Add a few samplesRegister samples or import a plate, and watch lineage and IDs get assigned automatically.
- Build a workflowModel one of your real workflows as steps and run it to see lineage build itself.
Startups, academic and core labs: contact us for special pricing. Full plans are on the pricing page.
FAQ
Questions about the LIMS.
What is the Cypher AI LIMS?
The Cypher AI LIMS is a laboratory information management system that tracks samples, materials and containers, and records every step done to them. Lineage builds as the work is logged, so any sample traces back to its source. It shares a platform with the Cypher ELN, analysis tools and AI agent.
How much does the Cypher LIMS cost?
The Cypher AI LIMS is included in two plans: Pro, at $50 per user per month, and Enterprise. It works inside a team. The Free plan includes the ELN but not the LIMS.
How does the Cypher LIMS track sample lineage?
Each workflow step in the Cypher LIMS links what went in to what came out, with volumes. A dilution, a plate transfer or an upload of plate reader results each becomes a step, and the lineage graph builds itself from those steps.
Can we import our sample inventory from spreadsheets?
Yes. Give the Cypher AI agent the spreadsheet, and it proposes the samples, containers and plate positions to create, plate layouts included. Nothing is written to the LIMS until you approve the plan, unless you switch the chat to Auto.
Does the Cypher LIMS track sample volumes?
Yes. Each sample in the Cypher LIMS has a remaining volume. Steps that use the sample deduct from it automatically, and the step builder warns you before a transfer would leave a well short.
Can the Cypher LIMS print barcode labels?
Yes. Every record gets an automatic ID, such as SPL-20260915-0034, and each container prints a QR label with its ID and name once a team admin turns on printing. Labels open as a PDF sized for a Dymo 3/4 × 2.5 inch label by default.
Does the Cypher LIMS keep an audit trail?
Yes. Samples, containers, materials and steps in the Cypher LIMS keep a field-level change history: the old value, the new value, who changed it and when.
Does the Cypher LIMS work with plate readers and liquid handlers?
Plate reader results upload as a CSV file. The Cypher LIMS matches each reading to the sample in its well and shows the plate as a heat map. Liquid handler support is in Beta and varies by vendor, so ask Cypher about yours.