hernandomv / czi-roisplitter

reads data from the Slide Scanner (.czi) and splits rois defined by user

czi-roisplitter

This script generates a Fiji GUI used to browse through .czi files coming from the Slide Scanner, displaying low resolution versions of the images, and allowing the user to select big ROIs, or to load ROIs from the Allen Brain Atlas assuming previous registration of the images with ABBA. It then splits the big ROIs into smaller images and saves them independently splitting each channel, at the resolution desired.

Installation

It depends on functions that are located in the following repo, so make sure you have them in your Fiji:

https://github.com/HernandoMV/czi-rs-functions

Either drag "czi_roisplitter.py" (inside "czi_roisplitter" folder) to Fiji and run it, or add it inside "Fiji.app/plugins" to have it as a plugin in your Fiji. You can add scripts like this one inside subfolders in "plugins" to have your Fiji->Plugins menu better organised:

Usage

It is used in larger pipelines like this one: https://github.com/HernandoMV/ph3-analysis

This is how the GUI looks:

TODO: write tutorial