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Measure_Nuclei_And_Membranes_Tool

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Volker edited this page Mar 16, 2022 · 1 revision

The tool takes the results of cell and nuclei segmentation done with cellpose [1] and transforms the cytoplasm selection into a membrane selections, removes rois for which one membrane does not match one nucleus and measures the membranes and nuclei in all channels but the nuclei-channel.

Montage.png table_part01.png table_part2.png

Getting started

To install the tool save the file measure_nuclei_and_membranes.ijm into the folder macros/toolsets of your FIJI installation.

Select the "measure_nuclei_and_membranes" toolset from the >> button of the ImageJ launcher.

toolset

  • the first button opens this help page
  • the o-button opens a batch script that converts cellpose results _cp_outlines.txt to rois in the overlays of the input images
  • the c-button transforms the cytoplasm selections into membrane selections
  • the m-button removes rois for which one membrane does not match one nucleus and measures the membranes and nuclei

How to use

Use our modified cellpose version to batch segment in two runs the nuclei and the cytoplasms of the cells and save the results into the same output folder. Press the o-button of the toolset and run the python-script from the editor to convert the cellpose outlines to ImageJ rois. The rois will be stored in the overlays of the input images. Press the c-button to transform the cytoplasm rois into membrane rois. Finally press the m-button to remove non-matching nucleus/membrane rois and measure the intensities in the membranes and nuclei in all channels but the nuclei channel.

Options

Right-click the c-button to open the options for the cytoplasm to membrane transformation

c_options.png

  • membrane diameter - the diameter of the membrane band-like rois
  • membrane channel - the channel containing the cell (cytoplasm) staining
  • file extension - the file extension of the input image files without the point, for example tif

m_options.png

  • nuclei channel - the channel containing nuclei, the intensities in this channel will not be measured
  • file extension - the file extension of the input image files without the point, for example tif

Literature

[1] Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x

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