ABBA-QuPath Registration Exporter

A Python app and Groovy script that helps export transformed cell detections from ABBA-registered data stored in QuPath projects.

Installation

Python version

This software has been tested on Python 3.9

First-Time Installation

pip install ABBA-QuPath-RegistrationExporter

Upgrading to Latest Version

pip install --upgrade ABBA-QuPath-RegistrationExporter

Running Software

To launch the programm and open the GUI

regexport

How to use

1. Download BIOP Extensions

Provide empty directory to download required files from BIOP

2. Get QuPath Exporter

Download and Save the .groovy script to download and to save .tsv file from QuPath.

Please provide a name and save it to the destination directory.

3. Load Brainglobe Atlas

When using for the first time, this button downloads the Brainglobe Atlas - it is currently using the allen_mouse_25um version.

Press the button to display the 3D view of the atlas and to load the whole hierarchy of the brain regions.

4. Load TSV Files

Provide the path the .tsv file(s) to load in the software, multiselection is required for multiple sections viewing.

5. Use the left-hand panel

When clicking on the brain (sub)region name, it will only display cells located in the chosen region.

Multiselection is possible to display different regions simultaneously.

6. Use the right-hand panel

• First drop-down menu is to select according to which criteria the colormap will be applied.

e.g. BrainRegion -> 1 color per different region

e.g. CustomColumns (from the .tsv file) -> 1 color per different value

• Second drop-down menu is to select the colormap.
• Figure displays Histogram and cumulative histogram from the selected content in the first drop-down menu.
• Sliders are to set up threshold according for each CustomColumns, and to ignore cells that are above those thresholds. The ignored cells will then be OFF on the brain atlas visualization. Only the cells that are visualized on the atlas will be saved in the last step

7. Save Cells

Provide the name and path to save the output result as .csv or .feather file. .feather file is a compressed version of .csv By default, it is saving the follogin content for each cells (position + custom columns + acronym/name of the finest sub-region area in the brain atlas + original image/.tsv file).

You can choose to save Selected cells only, in that case it is saving only the result for the displayed cells. The Acronym and BrainRegion fields will be the one selected in the hierarchy in the left-hand panel.

Running Tests

git clone https://github.com/nickdelgrosso/ABBA-QuPath-RegistrationAnalysis
cd ABBA-QuPath-RegistrationAnalysis
pip install -e .[dev]
python -m pytest