Image Analysis

Software Downloads

ZEN Lite is available for download from:

LAS X for Leica Thunder Imager 3D Tissue can be downloaded from:

FIJI open source software for image analysis:

QuPath an open source software for histological sample analysis

Analysis resources

Fiji scripts

Macro for extracting single tif files out of the lif project:

https://github.com/HGrobe/CTIU_Kuopio/blob/main/LIF_Extractor.ijm

Reading material and online resources for image analysis:

• “Introduction to Bioimage Analysis” by Pete Bankhead
  https://bioimagebook.github.io/index.html
  
• “Bioimage Data Analysis Workflows” by Kota Miura
  https://link.springer.com/book/10.1007/978-3-030-22386-1
  
• Online Tutorial for image analysis with FIJI:
  https://monashmicroimaging.github.io/gitbook-fiji-intermediate/chapter1.html
  
• YouTube Tutorial for image segmentation and filtering in FIJI
  https://www.youtube.com/watch?v=08SZnZBl4lM
  

Reading material and online resources for colocalization analysis:

• Image co-localization – co-occurrence versus correlation
  https://journals.biologists.com/jcs/article/131/3/jcs211847/77151/Image-co-localization-co-occurrence-versus
• Understanding Colocalization Coefficients
  https://www.scribd.com/document/680549608/Co-Localization
• A guided tour into subcellular colocalization analysis in light microscopy
  https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2006.01706.x
  

Reading material and online resources for tracking analysis:

• TrackMate documentation
  https://imagej.net/plugins/trackmate/index
• TrackMate webinar
  https://www.youtube.com/watch?v=ITwamUmna-Q
• CellTracksColab Wiki
  https://github.com/CellMigrationLab/CellTracksColab/wiki

If you need help with your analysis, don’t hesitate to reach out to us under:
[email protected]