CIF Tutorial | Fiji | Segmenting Muscular Fibers
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[Summary]
How to use Fiji along with MorpholibJ and StarDist to segment muscular fibers from a color slide scanner image.
NB : No method is perfect and this one is no exception. It can obviously benefit from further refinements like better filtering, and maybe manual label edition to correct obvious mistakes. There are also other methods involving cellpose and python for this specific task, but it's more complicated to implement for the beginners. (see below).
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[Notions viewed]
- Fiji and Image type, plugin installation, label images, measurements, scales
- StarDist
- MorphoLibJ
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[Images]
Gastrocnemius muscle cross sections, courtesy of Martino Guiotto, Pietro Di SUMMA group.
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[Links]
Fiji: imagej.net/software/fiji/
MorphoLibJ: imagej.net/plugins/morpholibj
StarDist: imagej.net/plugins/stardist
Alternative method (better results, a bit more complicated) : "Automatic and unbiased segmentation and quantification of myofibers in skeletal muscle" (www.nature.com/articles/s4159...)
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[Author]
Yannick Krempp, bioimage analyst at the CIF platform, Lausanne, Switzerland
cif.unil.ch
/ yannick-krempp
5 сен 2021