Metadata-Version: 2.4
Name: membrane-annotator
Version: 0.1.0
Summary: Generate membrane segmentations from vesicle and double membrane masks
Author: Justin Jung
Requires-Python: >=3.9
Requires-Dist: click
Requires-Dist: copick
Requires-Dist: numpy
Description-Content-Type: text/markdown

# Segmentation process
This runs locally membrane creation. 
Given some previous annotations on copick (that correspond to either double membranes or filled out objects), 
we create membrane annotations which we save to copick.

Usage: 
`python change_layers.py --run-id 19032 --session-id NAME_OF_ID_WITH_ANNOTATIONS`
Note: 
An object annotation should paint the entire object, where the membrane is constructed by considering the outer border. 
A membrane annotation corresponds to a double membrane, where the double membrane is processed by splitting into two. 


Example (from two object annotations): 
<img width="1728" height="1500" alt="image" src="https://github.com/user-attachments/assets/7eeae94b-e608-4b05-93db-367e95450b0f" />


### Further notes
The copick config `visicle_config_increment.json` should be used for the `nninteractive-launch --config`.
Each object (double membrane or entire blob that we should extract a border from) should correspond to one label. 
A single membrane (i.e requires no processing) should be labeled with label class type "single".
 

   
