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, you may follow the instructions in this post.
-
Latest firmware for main controller: https://github.com/Cephla-Lab/Squid/tree/master/firmware/octopi_firmware_v2/main_controller_teensy41
-
Latest firmware for joystick controller: https://github.com/Cephla-Lab/Squid/tree/master/firmware/octopi_firmware_v2/control_panel_teensyLC
- 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.
