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Cell segmentation and tracking

outline/content

  • Intro: description what we want to achieve, what the dataset consist and what operations and tools we use.

In this simple workflow, we will be showing how to use microSAM (link plus source) in combination with Trackmate Fiji (link plus source) plugin to track cell migration. The dataset consist of fluorescent images of MDA-MB-231 cells expressing and labeled against ERK activity and live recorded using a widefield fluorescence microscope [1, 2].

  • open and visualize dataset -> Napari (base)
  • split channels and save them in separate files -> Fiji
  • reopen the channel containing the cell nucleus staining (DAPI) with Napari micro-SAM
  • Adjust the setting for automatic segmentation.
  • segment the cells.
  • save the resulting mask (annotation) as an image
  • in fiji, merge the resulting mask with the original 2 channels image .

Resources

  1. https://zenodo.org/records/5205955
  2. https://www.nature.com/articles/s41592-022-01507-1