starchaea

notebooks for stardist x trackmate x archaea project

Data and models

E-mail me (Siân) if you want/need access to test datasets and trained models.

Model training - haven't included this. Don't know if it's worth making a separate notebook in this repo or just point people to Stardist training example? Will gather together some examples of annotated data for both channels either way.
Collated_process_up_to_trackmate.ipynb - I've tested this for all the example data, should be pretty stable.
Tracking_helper.ijm in Fiji (needs to have my_tracking.py in Fiji plugins folder). Probably not worth trying to call this from a notebook is it? I got a bit over excited when I realised that you can open Fiji from a jupyter notebook (Probably_a_bad_idea.ipynb). Maybe should have GUI options for settings inside my_tracking? E.g. gap lengths etc
Process_trackmate.ipynb - I've tested this on 2 colour data but not single colour data.
Curation_helper.ijm in Fiji. This is optional, instructions for use are provided at end of Process_trackmate.ipynb.
Measure_polygons.ipynb - again, I've tested this on 2 colour data but not single colour.

https://www.youtube.com/watch?v=jyO-MyJ4R1g - I LOVE this song and also it's by Starcadian which is basically starchaea :)