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Image Analysis and Data Management

Image Analysis

Bio-Imaging Resource Center provides a variety of image analysis resources/training:

  • One-on-one user imaging data discussion, where we suggest the best software/method/pipeline for image analysis
  • Writing of custom image analysis scripts, pipelines, batch processing
  • Regular image analysis seminars and workshops
  • Image Analysis User Group meetings
  • One-on-one user training
  • Helpdesk session, every Wednesday, 3-5pm

In addition, we encourage our users to contact us at the experimental design stage to have a discussion with our team of microscopy and image analysis experts, to ensure that the imaging data acquired will be appropriate for the planned analysis and research questions


We have expertise in a variety of image analysis software/tools, which we use to help analyze our users’ imaging data

Open-source software: ImageJ/Fiji, QuPath, Napari, CellProfiler, Icy

Commercial Software: Imaris, Arivis, Aivia, Huygens, MetaMorph

Machine/Deep Learning frameworks: Weka, ilastik, Labkit StarDist, Cellpose, DeepImageJ, ZeroCostDL4Mic

For more information, please visit our Bio-Image Analysis GitHub page.

Here are the details on the available workstations and software for image processing and analysis.

Data Management

User data is transferred from the microscope acquisition computer to the BIRC server, which is for temporary storage and transfer, not for user data storage purpose. Users are advised to back up their data to their own computers/external hard drives ASAP.

Here is a list of the file formats for images acquired on different BIRC microscopes and the relevant data handling procedures:

  Microscope name  Manufacturer  BIRC nickname  File format  Data handling 
1  Wide-field fluorescence/brightfield/DIC microscope  Zeiss  Edwina  .tif  MetaVue acquisition software (Molecular Devices) 
2  Widefield fluorescence and phase contrast microscope for live time-lapse imaging  Olympus  Wendolene  .tif  MetaMorph acquisition software (includes MDA) 
3  DeltaVision Image Restoration Microscope  Applied Precision/ GE/Leica  Wallace  .dv  SoftWoRx acquisition software 
4  DeltaVision Image Restoration Microscope with FRAP/photoactivation module and environmental chamber  Applied Precision/ GE/ Leica  Totty  .dv  SoftWoRx acquisition software 
5  CellDiscoverer7 (CD7) automated widefield high-throughput system  Zeiss  Admiral Collingwood  .czi  Zeiss ZEN Blue acquisition software 
6  LSM 980 with Airyscan 2 – Confocal Microscope  ZEISS  Molly  .czi  Zeiss ZEN Blue acquisition software 
7  Inverted LSM 780 laser scanning confocal microscope  Zeiss  Technotrousers  .czi  Zeiss ZEN Black acquisition software 
8  Inverted LSM 880 Airyscan NLO laser scanning confocal and multiphoton microscope  Zeiss  Rocky II  .czi  Zeiss ZEN Black acquisition software 
9  RS-G4 resonant scanning confocal system  Caliber ID  Cutlass Liz  .tif


RS-G4 acquisition software 
10  Facility Line STED/confocal system  Abberior  Pirate King  .obf 


Acquisition software 1: Imspector (Lightbox), ver 16.3.14287-w2129 

– generates images in the .obf format 

Acquisition software 2: Imspector (BASE), ver 16.3.14287-w2129 

– generates images in the .msr format 


.obf and .msr files can be opened in either of the above acquisition software or Fiji 

11  InstantSIM (iSIM) super-resolution system with Mizar TILT light-sheet  VisiTech/ BioVision/ Leica/ Mizar  Scopey McScopeface  .nd



VisiView acquisition software 
12  OMX Blaze 3D-SIM super-resolution microscope  Applied Precision/ GE/ Leica  Reverend Hedges  .dv  SoftWoRx acquisition software 
13  FV1000MPE upright multiphoton system  Olympus  Philip  .oif  Fluoview acquisition software 
14  Spinning disk confocal microscope  Zeiss/ Yokagawa/ Spectral Applied  Bunty  .nd 


MetaMorph acquisition software 
15  CellVoyager spinning disk confocal  Yokagawa/ Olympus  HMSBeagle  .tif  Acquisition software: CV1000 

Single TIF files stitched with custom Fiji macros provided by the BIRC. 

16  Widefield/TIRF system  Nikon  Piella  .nd2  Elements acquisition software 
17   Ultramicroscope II Light sheet  LaVision/ Miltenyi BioTec  Polly  OME-TIFF  Acquisition software: ImspectorPro 

Imaris for assembling the images