New brainmapper napari widget released#
One common use of BrainGlobe tools is to analyse the distribution of cells in a whole brain image. This process
involves first detecting cells using cellfinder and then registering (aligning) the
data to a BrainGlobe atlas using brainreg. The detected cell positions must then be
transformed from the coordinate space of the raw data to the coordinate space of the atlas for analysis.
This workflow has previously been implemented with the brainmapper
command line tool, which runs brainreg, then cellfinder and then analyses the distribution of cells throughout
the brain. This tool is excellent for automated analyses, but using a command-line tool isn’t very intuitive for many
users, and it is difficult to optimise parameters for a new application.
brainreg and cellfinder both have napari plugins. This allows use within a graphical user interface, and makes
it easier to iteratively optimise parameters. However, to assign cells to a brain region, users had to use the
brainmapper command line tool.
To improve this we have released a new brainmapper napari widget.
This allows users to combine the results of
brainreg and cellfinder to analyse the distribution of cells across the brain.
What does it do?#
The plugin takes as input cell coordinates (from cellfinder or another tool) and a brainreg output directory. It
then transforms cells to the atlas space. A summary of the cellular distribution (i.e. cells per brain region) is
then displayed:
structure_name |
left_cell_count |
right_cell_count |
|---|---|---|
Retrosplenial area, ventral part, layer 5 |
1853 |
814 |
Lateral dorsal nucleus of thalamus |
1541 |
0 |
Retrosplenial area, ventral part, layer 2/3 |
163 |
686 |
Retrosplenial area, dorsal part, layer 5 |
561 |
82 |
Retrosplenial area, dorsal part, layer 2/3 |
194 |
245 |
Ventral anterior-lateral complex of the thalamus |
412 |
0 |
Example of the results displayed within napari after running the widget
Full analysis results (coordinates of every cell, and numbers of cells for every brain region) can be saved alongside the transformed cell coordinates.
How do I install it?#
The widget is part of the brainglobe-utils package. However, the easiest way to install it is to upgrade the
brainglobe package:
pip install brainglobe --upgrade
It can also be installed from the
napari plugin manager
by searching for brainglobe-utils.
How do I use it?#
Please see the documentation and the analysing brainwide distribution of cells tutorial.