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CBI-MMTools: Micro-manager Microscopy Synchronized Camera and Illumination Control Tools


CBI-MMTools is a set of plugins, device adapters and libraries for the operation of microscopy platforms using Micro-Manager.

CBI-MMTools is a set of tools designed for the Micro-Manager microscopy software. It provides libraries, plugins and drivers to control various acquisition devices (i.e. LED illumination, light-camera synchronization, 4D motorized stage control). This allows to implement diverse acquisition methods that require precise hardware control. These tools have been integrated in the custom OpenSPIM microscopy platform at Idiap Research Institute.



  • Unequivocal cardiac phase sorting from alternating ramp- and pulse-illuminated microscopy image sequences - Idiap Publications [] (
  • Marelli, F and Liebling, M. (2023) Efficient compressed sensing reconstruction for 3D fluorescence microscopy using OptoMechanical Modulation Tomography (OMMT) with a 1+2D regularization (submitted)
  • Marelli, F. and Ernst, A. and Mercade, N. and Liebling, M. (2023) PAAQ: Paired Alternating AcQuisitions for Virtual High Frame Rate Multichannel Cardiac Fluorescence Microscopy (submitted)


  • Repository GitHub - idiap/CBI-MMTools: Plugins, device adapters and libraries for the operation of microscopy platforms using Micro-Manager, developed by the Computational BioImaging group at Idiap Research Institute (Fran├žois Marelli, current 6/2023)
  • The above extend and superceed the tools distributed in: GitHub - idiap/hesm_distrib: Temporal Super-Resolution Microscopy Using a Hue-Encoded Shutter, Christian Jacques (which are directly linked to patent)


  • Compatibility with leading (and possibly only) open source microscopy driver software
  • Flexibility
  • Extensibility


Live optical 3D microscopy: - Biology - Materials characterization - Photography

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