brainreg
brainreg copied to clipboard
brainglobe
Automated 3D brain registration with support for multiple species and atlases.
Once https://github.com/brainglobe/brainreg/pull/68 is merged a GH actions job should be added that installs niftyreg from conda. This should show up as increased coverage, as it will hit the code paths...
- [ ] Identify potential corrupted files before proceeding with registration (based on file size) - [ ] Identify corrupted files on loading (and report to user), exit gracefully -...
As with amap, see https://github.com/SainsburyWellcomeCentre/amap-python/issues/56
If not in debug mode, intermediate files should be deleted as soon as they are not required, not all at the end, saving disk space.
In atlases that have provided an additional reference stack, allow the user to select which reference stack in the atlas they would like to apply the registration to.
Before submitting a pull request (PR), please read the [contributing guide](https://github.com/brainglobe/.github/blob/main/CONTRIBUTING.md). ## Description Begin to implement custom exceptions as mentioned in brainglobe/brainreg#82. Started by a custom exception for failed file...
Results in the following error running Windows 10 in Pycharm (pip install): (test_brainreg_dev) C:\fMRIData\git-repo\brainreg>pip install -e '.[dev]' ERROR: '.[dev]' is not a valid editable requirement. It should either be a...
**Describe the bug** I successfully registered the new Princeton mouse brain atlas to our data (1st image), but the output file corresponding to our atlas-registered data appears to have a...
**Describe the bug** [Opening an image stack with "Open files as stack" and then running brainreg in napari on the stack fails with trace below](https://forum.image.sc/t/use-registered-atlases-from-brainreg-for-segmentation-in-imaris/86206/65?u=alessandrofelder) ```bash --> 446 run_niftyreg( registration_output_folder...
This should either be prevented (e.g. check the image size) or the user should be warned.
Metadata
Owner
Metadata
Automated 3D brain registration with support for multiple species and atlases.