Alessandro Felder
Alessandro Felder
Currently, we assume the segmentation is anchored in (0,0,0).
**Is your feature request related to a problem? Please describe.** By default, not all tests are run, neither in a local development environment nor on CI. You need to specify...
**Describe the bug** streamlines example test fails with URL not found: Forbidden **To Reproduce** 1. Run `pytest -vv tests/test_examples.py --runslow --runlocal` (MacOs M2 on https://github.com/brainglobe/brainrender/commit/8866e3a762476820c20cc52994e5e3a3cc21c199 with vedo 2023.4.6) 2. Output...
The text below was removed from the `brainglobe-segmentation` tutorials, but may be handy as an example for `brainrender` or `brainrender-napari` one day: >if you loaded your data in atlas space,...
**Is your feature request related to a problem? Please describe.** A user reports that running cellfinder through napari takes 2 days on their machine, but only 1 day through the...
**Is your feature request related to a problem? Please describe.** In cell candidate detection, we set aside two very high integer values (currently SOMA_CENTRE_VALUE as `np.uint16.max-1` and THRESHOLD as `np.uint16.max-2`)...
Don't think this is a priority right now, but it feels weird to me to hardcode html into Python fstrings. Would there be a better solution?
Given that cellfinder can take a while to run, we should check for valid inputs before running the computationally expensive parts. Currently, we can e.g. input to keep more CPUs...
* Document edge cases (like "no cell candidates found"). * Handle edge cases (like "Don't try to run classification if there are no candidate cells to classify, but rather throw...
### how to reproduce 1. open `detect` widget 1. open example images *after* opening widget. 1. rename the images 1. Most recently renamed image still shows with old name in...