Our open hardware bioimaging platform for fluorescence microscopy and Raman spectroscopy based on the SQUID/OCTOPI 60x60mm inverted microscopy stage
Squid (Simplifying Quantitive Imaging Development and Deployment) provides a full suite of hardware and software components for rapidly configuring high-performance microscopes tailored to users' applications with reduced cost, effort and turnaround time. Besides increasing accessibility of research microscopes and available microscope hours to labs, it is also designed to simplify development and dissemination of new or otherwise advanced microscopy techniques. Applications include slide scanner for digital pathology, time lapse imaging with 2D or 3D tiling, spatial omics that involves multicolor and multi-round imaging, tracking microscopy,computational microscopy, including label free microscopy using phase/polarization/reflectance + deep learning, and super resolution microscopy.
- [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 ]
- main software repo: GitHub (this repo)
- 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
- Eearly Results, Related Work and Possible Applications www.squid-imaging.org
- Forum to discuss instructions: https://forum.squid-imaging.org
- Spin-off company: https://cephla.com/product/squid/
Is based on the SQUID/OCTOPI 60x60mm inverted stage.
| Filter | Type | supplier |
|---|---|---|
| FF458-Di02-25x36 | Beamsplitter 458 to couple in 405nm LED | AHF |
| FF520-Di02-25x36 | Beamsplitter 520 to couple in 470nm LED with 635nm LED | AHF |
| ZT405/488/561/640rpcv2-UF3 | 4-band fluorescence beamsplitter | Chroma |
| FF01-446/523/600/677-25 | 4-band blocking filter for all fluorescence channels | Laser2000 |
| ZET405/488/561/640xv2 | 4-band illumination filter (20mm) | Chroma |
| ZT775sp-2p-UF3 | Beamsplitter brightfield to add on 785nm Raman | Chroma |
| F46-950 (RT785rdc + RET785/6x + RET792LP) | 785 nm Raman Filterset with Beamsplitter, Bandpass and Emitter | AHF |
Inspired by the Benchtop mesoSPIM light sheet microscope, we have incorporated the ZWO-asto mini electronic filter wheel (EFW) with the following filter selections:
| Position | Filter | Type | supplier |
|---|---|---|---|
| #1 - All | none | The four bands of the multiband blockig filter are visible simultaneously | |
| #2 - Blue | 447/60 BrightLine HC | Filter blue, e.g. DAPI stain | AHF |
| #3 - Green | 525/39 BrightLine HC | Filter green, e.g. sfGFP | AHF |
| #4 - Orange | 600/37 BrightLine HC | Filter organge | AHF |
| #5 - Red | 635 LP Langpass-Filter | Filter red , e.g. PI stain | AHF |
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