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SiMoRa - SQUID Microscope with Raman Open Source Love

Our open hardware bioimaging platform for fluorescence microscopy and Raman spectroscopy based on the SQUID/OCTOPI 60x60mm inverted microscopy stage

What is the SQUID Microscope?

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 ]

SQUID resources from the creators

Our custom implementation

Is based on the SQUID/OCTOPI 60x60mm inverted stage.

Optical filters used

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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Control files of our SQUID fluorescence microscopy platform.

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