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Tracking Organoids

  • Home
  • Getting started
    • Downloading example data
    • Setting up Anaconda
  • Cell segmentation
    • Manual segmentation
    • Using CellPose
    • Classical segmentation
  • Cell tracking
    • Cell tracking using a flow-solver
  • Visualizing organoids
    • 3D renders using PyVista
    • Depth-colored images
    • Opening images in Napari

Cell segmentation

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  • Manual segmentation – cumbersome, useful in some cases.
  • CellPose tutorial – if this works out of the box, then you’re done.
  • Classical segmentation – gives you more control, and no need for training data.

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Contact

Rutger Kok
rutger@rutgerkok.nl

Researcher in the Maria Rodriguez Colman Lab

  • Home
  • Getting started
    • Downloading example data
    • Setting up Anaconda
  • Cell segmentation
    • Manual segmentation
    • Using CellPose
    • Classical segmentation
  • Cell tracking
    • Cell tracking using a flow-solver
  • Visualizing organoids
    • 3D renders using PyVista
    • Depth-colored images
    • Opening images in Napari