Enrich developer experience

vibbic / biosegment

BioSegment is a software stack to enable segmentation of microscopy data using machine learning models.

https://vibbic.github.io/biosegment/

GNU General Public License v3.0

4 stars 2 forks source link

Enrich developer experience #11

Open berombau opened 4 years ago

berombau commented 4 years ago

The developer experience still lacks:

[ ] an example dataset folder
- now they are copied manually between developers. Maybe adding the EMBL as example. The model can be trained from scratch and would be too large to include in VCS.
[x] Windows support
[ ] Environments that an IDE can use to do code analysis. e.g. a Python interpreter with all packages for backend, frontend... VS Code is probably the most popular IDE and should be supported first.

JorisRoels commented 4 years ago

Maybe take another example dataset than EMBL, because that's a private dataset and the software would eventually go open source. I think the EPFL dataset is a good alternative and there's a good reference as well: https://www.epfl.ch/labs/cvlab/data/data-em/

berombau commented 4 years ago

I added TIFF support so the EPFL dataset can be read directly by the viewer.

For supporting different data folders between developers, I was thinking of describing the layout of the data folder in a .yaml and allowing BioSegment to modify its database on startup based on the contents of this file. Then all dataset specifics can be removed from the biosegment source code (init_db.py in backend) and new developers can create a new data folder with scripts/create-data-folder.sh.