The monorepo for the robots in our robotlabs for cell painting and imaging.
The cell painter system controls the dispenser from BioTek and washers from Biotek and BlueCatBio as well as the incubator using the universal robots robot arm. Here is an overview:
The standard operating procedure is here: sop-cellpainter.md.
The imager system controls the Squid microscope and the Nikon microscope as well as the fridge using the precise flex robot arm. Here is an overview:
The standard operating procedure is here: sop-imager.md.
| machine | os | room | ip |
|---|---|---|---|
| Ubuntu NUC | ubuntu | the cage | 10.10.0.55 |
| Windows NUC | windows | the cage | 10.10.0.56 |
| Nikon stage computer | raspian | squikon | 10.10.0.72 |
| Nikon NIS computer | windows | squikon | 10.10.0.76 |
| Squid Mikro Asus | ubuntu | squikon | 10.10.0.95 |
| "GBG" computer | windows | squikon | 10.10.0.97 |
| PF robotarm | - | squikon | 10.10.0.98 |
| UR robotarm control box | linux | the cage | 10.10.0.112 |
The node names and IP-addresses are also specified in labrobots/labrobots/__init__.py.
The project consists of a few packages:
| cellpainter | Cell painter program and control of the Universal Robot (UR) robotarm. Microscope imager program and control of the PreciseFlex (PF) robotarm. |
|---|---|
| labrobots | Remote control of non-robotarm robots: liquid handling machines, incubator, fridge, microscopes and barcode scanners. |
| flash_pf | Code to flash the PreciseFlex (PF) robotarm with our modified software. |
It also includes two utility packages:
| viable | Library for writing web frontend code in python. |
|---|---|
| pbutils | Shared utilities such as bridging dataclasses and sqlite3. |
External dependencies:
| flask | Micro framework for building web applications. |
| z3-solver | SMT-solver used in the robotlab scheduler. |
| apsw | Another python sqlite3 wrapper, needed for precise control of sqlite3 version. We need all json extensions. |
| pyserial | COM-port communication with barcode scanner and bluewasher. |
| RPi.GPIO | GPIO-communication with RPi for the Nikon automated stage. |
The BioTek control code require a C# program that needs to be separately built.
On the ubuntu NUC that will run the guis and schedulers, install python >= 3.10 and:
./foreach.sh pip install --editable .
On each windows machine that runs labrobots, install python >= 3.10 and:
pip install --editable labrobots
Further instructions are in under labrobots/
Github actions is set up, check .github/workflows/test.yml.
One way to run this locally is to use act.
The gui is run on the ubuntu NUC. To make it easier to find it we alias its hostname.
On windows, for example the BioTek computer, add this line to C:\Windows\System32\drivers\etc\hosts
10.10.0.55 cellpainter
On ubuntu, for example the squid mikro asus computer, add this line to /etc/hosts
10.10.0.55 imager
To enable showing diffs of sqlite databases when running git commands you can follow https://stackoverflow.com/questions/13271643/git-hook-for-diff-sqlite-table
One way to ignore big blobs is adding this to git config:
[diff "sqlite3"]
binary = true
textconv = "dump(){ sqlite3 -batch \"$1\" .dump | sed \"s,X'\\([0-9a-f]\\{16\\}\\)[0-9a-f]*',X'\\1...',g\"; }; dump"
You will need to add this to git attributes:
*.db diff=sqlite3