The Squid repo provides firmware and software for controlling Cephla's Squid microscope.
Applications include:
- Slide scanning
- Live Cell Imaging
- High Content Screening
- Optical Pooled Screen
- Spatial Omics (with fluidics integration)
- Organoids
- Expansion Microscopy and more...
Specifications of Squid microscope: link
Follow the most recent development and share how you use Squid on Cephla forum
See related work and applications on: www.cephla.com, www.squid-imaging.org
Ubuntu 22.04 is the most tested platform. Other Linux systems should work but performance is not guaranteed.
See README in /software directory for instructions. Toupcam and laser auto-focus camera dependencies will be installed automatically when you run the setup script.
After installation, you can run python3 /software/tools/script_create_desktop_shortcut.py to create a shortcut on Desktop.
See this post on Cephla forum for Windows instructions.
If your Squid has a laser auto-focus module, you will need to install the driver for the laser auto-focus camera and reboot the computer. You may also need to install the driver for the main camera you use.
After installation, you can follow this post to create a shortcut on Desktop.
See the image-stitcher repo
Software SOP: link
Fluidics acquisition SOP: link
New version coming soon!
Usually firmware should be already uploaded to the controller. If you do need to re-upload firmware, see the firmware README for instructions.
This repository uses git submodules for external dependencies. After cloning, initialize submodules:
# Clone with submodules (recommended)
git clone --recursive https://github.com/Cephla-Lab/Squid.git
# Or initialize after clone
git submodule update --init --recursiveSubmodules:
| Path | Repository | Description |
|---|---|---|
software/control/ndviewer_light |
ndviewer_light | Lightweight NDV-based image viewer |
software/fluidics_v2 |
fluidics_v2 | Fluidics control |
Updating submodules:
# Update a specific submodule to latest
git submodule update --remote software/control/ndviewer_light
git add software/control/ndviewer_light
git commit -m "chore: update ndviewer_light submodule"
- tracking software repo: GitHub
- CAD models/photos of assembled squids: Google Drive
- BOM for the microscope, including CAD files for CNC machining: link
- BOM for the multicolor laser engine: link
- BOM for the control panel: link
[1] Hongquan Li, Deepak Krishnamurthy, Ethan Li, Pranav Vyas, Nibha Akireddy, Chew Chai, Manu Prakash, "Squid: Simplifying Quantitative Imaging Platform Development and Deployment." BiorXiv [ link | website]
[2] Deepak Krishnamurthy, Hongquan Li, François Benoit du Rey, Pierre Cambournac, Adam G. Larson, Ethan Li, and Manu Prakash. "Scale-free vertical tracking microscopy." Nature Methods 17, no. 10 (2020): 1040-1051. [ link | website ]
The Original Squid software was developed with structuring inspiration from Tempesta-RedSTED. The laser engine is inspired by https://github.com/ries-lab/LaserEngine.