Instrument data upload
Cypher AI File Agent
Upload instrument data automatically and kick off analysis in Cypher AI, even while you sleep. The File Agent watches the folder where almost any instrument saves its results and sends each finished run to Cypher AI, Google Drive or Google Cloud Storage.
For Windows 10 and 11. Installs on the instrument PC with our installation wizard.
Instrument PC D:\Instrument Data
- 2026-09-26_EXP-2510.4 MB41.3 MBRunningFinishedUploaded
- 2026-09-25_EXP-25039.8 MBUploaded
- 2026-09-24_EXP-24940.6 MBUploaded
Cypher AI Instrument Data / BLI
- 2026-09-26_EXP-25141.3 MB
- 2026-09-25_EXP-25039.8 MB
☁️ Uploaded 2026-09-26_EXP-251 to Cypher Files
What it does
Instrument data where your team can use it.
Install it once on the PC next to the instrument. After that, each run uploads on its own.
Waits for the whole run
Uploads once the files stop changing, so each run arrives complete.
Picks up after restarts
Remembers every run, retries failed uploads and skips runs it already sent.
Tells you in Slack
Posts each upload, and flags any run it can't read.
Analysis while you sleep
With Cypher AI, a widget can analyze each run as it lands.
The problem
In many small labs, instrument data still moves by USB stick.
Someone has to remember
Each run waits on a person with a USB stick, a shared drive or an email to themselves.
Runs end overnight
A long run can finish at 2 AM. The data sits on the instrument PC until morning.
Big platforms, big projects
Lab data platforms built for large pharma often expect a fleet of instruments and an IT team to run them.
Cypher AI is committed to giving small teams all the tools they need. The File Agent is the one for instrument data: every run, off the instrument and in one place.
How it knows
It uploads when the run is done.
Most instruments don't announce the end of a run. The agent checks the folder every minute and waits for the files to stop changing.
- Nothing to set up on the instrument itself.
- A run counts as done after 5 checks in a row with no change.
- If it can't read every file, it holds the run and tells you in Slack.
| Name | Size | Uploaded |
|---|---|---|
| 2026-09-26_EXP-251 | 41.3 MB | Sep 26, 1:13 PM2Each run gets its own folder, named the way the instrument named it. Subfolders come along. |
| ReportTemplate | Sep 26, 1:13 PM | |
| Run data files | 41.3 MB | Sep 26, 1:13 PM |
| instrument-upload-complete.txt | 0 B | Sep 26, 1:13 PM3A completion file goes in last, so your scripts and pipelines can tell the run is whole. |
| 2026-09-25_EXP-250 | 39.8 MB | Sep 25, 2:41 PM |
| 2026-09-24_EXP-249 | 40.6 MB | Sep 24, 3:05 PM |
Where runs land
Each run lands in your Cypher AI project.
- You choose the project and folder when you install.
- Each run gets its own folder, named the way the instrument named it. Subfolders come along.
- A completion file goes in last, so your scripts and pipelines can tell the run is whole.
Using Google instead? Send runs to a Google Drive folder, a shared drive or a Cloud Storage bucket.
Your runs sit next to the rest of your team's work.
File Agent APP1A check-in at the hours you pick. If something is wrong, it says so and lists what.
🔬 BLI: 💓 file-agent alive — uptime 12d 4h 51m, RSS 86.2 MB, heap 29.4 MB/41.0 MB
8:02🔬 BLI:2Give each PC its own label, so one channel can cover several instruments. 🧫 New BLI run detected: 2026-09-26_EXP-251
10:41🧪 Plate reader: ☁️ Uploaded ELISA_plate-03-20260926T144102Z-3f9a1c7e2b40.xlsx to Cypher Files
1:12🔬 BLI: ✅ Run finished: 2026-09-26_EXP-251 (41.3 MB). Uploading to Cypher Files…
1:13🔬 BLI: ☁️ Uploaded 2026-09-26_EXP-251 to Cypher Files3New run, finished, uploaded: one line each, in the channel you choose.
Status
Slack tells you what happened.
- A check-in at the hours you pick. If something is wrong, it says so and lists what.
- Give each PC its own label, so one channel can cover several instruments.
- New run, finished, uploaded: one line each, in the channel you choose.
Errors repeat every hour until they're fixed, then an all-clear follows.
You hear about a stuck run the day it happens.
Existing installations keep their current destination unless you select another one.
Setup
Set up in one sitting.
- One signed installer from Cypher. Nothing else to install on the PC.
- Pick where runs go: a Cypher AI project, Google Drive or Google Cloud Storage.
- Before it starts, it tests the instrument folder and the destination, so problems show up while you're at the PC.
- Change settings later from the Start menu.
- IT can install it silently with a script.
Instruments
Works with almost any instrument that saves files.
The File Agent reads what your instrument already writes to disk. You pick the kind of output when you install.
| What the instrument writes | For example | When the File Agent uploads |
|---|---|---|
| A new folder for each run | A BLI instrument's run folder | Once the folder holds data and sits unchanged for 5 checks in a row |
| A file for each result, in any format | A plate reader's CSV or XLSX exports | Once the file stops changing. Edited files can upload as new, dated versions. |
| A database file that grows during the run | An SPR instrument's run file | Once it stops growing with no write in progress |
Tested so far on Gator Bio BLI, Carterra SPR, and BioTek Synergy H1 and Cytation 5 plate readers.
Get started
Two ways to use it.
With Cypher AI
Runs go straight into your project
Your team finds each run in Cypher AI, next to its ELN and LIMS work, and a widget can analyze it as it lands.
- Book a 15-minute demo and tell us your instrument.
- Create an API key in Cypher AI.
- Run the installation wizard on the Windows instrument PC.
- Your next run shows up in the project.
On its own
Runs go to your Google storage
Keep using the Drive folder or Cloud Storage bucket you already have.
- Book a 15-minute demo and tell us your instrument.
- Share the folder or bucket with a Google service account.
- Run the installation wizard on the Windows instrument PC.
- Your next run shows up in Google Drive or Cloud Storage.
FAQ
Questions labs ask.
Updated September 28, 2026
What is the Cypher AI File Agent?
The Cypher AI File Agent is a Windows service that uploads finished runs from almost any lab instrument that saves files. It watches the instrument's output folder, waits until each run stops changing, and sends it to a Cypher AI project, Google Drive or Google Cloud Storage. In Cypher AI, a widget can analyze each run as it lands. Cypher AI built it for small teams that want their instrument data in one place without a data engineering project.
Which instruments does the File Agent work with?
The File Agent works with almost any instrument that saves its results as files. It handles instruments that write a new folder for each run, a file for each result in any format, or a database file that grows during the run. It has been tested on Gator Bio BLI, Carterra SPR, and BioTek Synergy H1 and Cytation 5 plate readers.
How does the File Agent know when an instrument run is finished?
The File Agent checks the output folder every 60 seconds and treats a run as finished once its files stop changing. For instruments that write a folder per run, the folder has to hold at least 1 MB and look the same for 5 checks in a row. For a database file that grows during the run, such as a Carterra SPR .sprdata file, there also has to be no write in progress.
Where does the File Agent upload runs?
The File Agent uploads each finished run to the destination you pick at install: a folder in a Cypher AI project, a Google Drive folder or shared drive, or a Google Cloud Storage bucket. Every run gets its own folder under the instrument's run name. The agent adds an instrument-upload-complete.txt file last, so scripts can tell the upload is whole.
What happens if the network or PC goes down during an upload?
The File Agent picks up where it left off. It records the state of every run in a local database, so after a restart it retries unfinished uploads and skips runs it already sent. If it can't read a folder, it posts a Slack warning and repeats it every hour until the folder reads again.
What does the File Agent need to run?
The File Agent needs a Windows 10 or 11 (64-bit) PC that can read the instrument's output folder and reach the upload destination. The installation wizard sets it up and includes everything else it needs, so nothing has to be installed first. IT teams can also install it silently from a script.
Does the File Agent have file size limits?
Uploads to Cypher AI accept files up to 250 MB each. Some instruments write bigger files: a 24-hour Carterra SPR run can reach about 370 MB. Files that size usually go to Google Drive or Google Cloud Storage instead.