Skip to content

Latest commit

 

History

History
52 lines (34 loc) · 2.39 KB

README.md

File metadata and controls

52 lines (34 loc) · 2.39 KB
Raw
description
Detecting cells in napari

Cell detection

Loading data

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

{% hint style="info" %} A widget should be 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. {% endhint %}

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 autofluroescence).

{% hint style="info" %} There are many napari plugins for loading data. By default, single 3D tiffs, and directories of tiffs can be loaded. {% endhint %}

Setting parameters

There are many parameters that can be set (see Parameters to set), but the following options must be set before running the plugin

Mandatory

  • 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.

{% hint style="info" %} It is likely that the classification will not perform well on new data, to improve this, see Training data generation. {% endhint %}

Saving data

The cell coordinates can be saved using any napari plugin (e.g. to csv). To save the cell coodinates 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)