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Cell detection#

Loading data#

Once napari, and the cellfinder plugin is installed, open napari, and load the plugin (Plugins -> cellfinder -> Cell detection).


A widget should then be docked into the side of your napari window. If this doesn’t happen, check for any errors (Plugins -> Plugin Errors, then select the cellfinder plugin from the drop-down menu). This error can be used to report problems on the GitHub page, or the help forum, see sidebar for links.

Then load your data (e.g. using the File-> menu, or by dragging and dropping data). There must be two registered channels; a signal channel (containing fluorescently labelled cells), and a background channel (containing only autofluorescence).


There are many napari plugins for loading data. By default, single 3D tiffs, and directories of tiffs can be loaded.

Setting parameters#

There are many parameters that can be set (see All cell detection parameters), but the following options must be set before running the plugin.

Mandatory parameters#

  • Signal image - set this to the image layer containing the labelled cells

  • Background image - set this to the image layer without cells

  • Voxel size (z) - in microns, the plane-spacing (from one 2D section to the next)

  • Voxel size (y) - in microns, the voxel size in the vertical (top to bottom) dimension

  • Voxel size (x) - in microns, the voxel size in the horizontal (left to right) dimension

Running cellfinder#

Click the Run button. The plugin will then run (this may take a while if you’re analysing a large dataset), and will produce two additional image layers:

  • Detected - these are the cell candidates classified as cells

  • Rejected (hidden by default) - these are the cell candidates classified as artefacts.


It is likely that the classification will not perform well on new data, to improve this, see Training data generation.

Saving data#

The cell coordinates can be saved using any napari plugin (e.g., to csv). To save the cell coordinates in the cellfinder XML format:

  • Select the Points layers (e.g. Detected and Rejected)

  • Click File -> Save Selected Layer(s)

  • Save with .xml extension (e.g. cells.xml)