brainlit
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neurodata
Method container for computational neuroscience on brains.
New users ran into issues installing the brainlit repo as a package when using Windows. Errors are detailed in Issue#124, update the README.md with a brief note to account for...
[log.txt](https://github.com/neurodata/brainlit/files/5205131/log.txt) I tried to run the brainlit tutorial, but I stuck at step#2. The url address I put is: ```"s3://mouse-light-viz/precomputed_volumes/brain1"``` but the error shows that the file cannot be found...
from @jovo (full disclosure not currently aware of what this means)
The goal of this will be to start getting estimates of how long it takes to run a soma detection algorithm on the complete brain images. By default, we will...
Downloading multiple chunks of data from s3 takes a long time, and is often the slowest step in a pipeline by far. For example, ``` from brainlit.utils.session import NeuroglancerSession sess...
Reformat the code in [base.py](https://github.com/neurodata/brainlit/blob/feature_rename/brainlit/feature_extraction/base.py), [neighborhood.py](https://github.com/neurodata/brainlit/blob/feature_rename/brainlit/feature_extraction/neighborhood.py), and [linear_features.py](https://github.com/neurodata/brainlit/blob/feature_rename/brainlit/feature_extraction/linear_features.py). Additionally, refactor and overhaul [test_subneighborhood.py](https://github.com/neurodata/brainlit/blob/feature_rename/tests/archive/test_subneighborhood.py) according to the standards mentioned in the [Refactor](https://github.com/neurodata/brainlit/projects) project. This means: - typing hints on every method...
As the repo is refactored (see the [Reformatting project](https://github.com/neurodata/brainlit/projects/1)), pep484 type hints are being added (example [here](https://github.com/neurodata/brainlit/blob/continue_upload/brainlit/utils/upload.py#L97)). [Typeguard](https://github.com/agronholm/typeguard ) allows for type checking via pep484 type hints, and using them...
CloudVolume will sometimes hang randomly, interrupting large uploads. Currently, if an error happens, we only print a short error message, and the upload must be restarted from scratch. It would...
Reformat the [code](https://github.com/neurodata/brainlit/blob/develop/brainlit/utils/swc.py) and [tests](https://github.com/neurodata/brainlit/blob/develop/tests/test_swc.py) to be similar to [upload.py]() and [session.py](). This means: - [ ] typing hints on every method and class - [ ] google-formatted docstrings on...
Reformat the code in [preprocess.py](https://github.com/neurodata/brainlit/tree/develop/brainlit/preprocessing/preprocess.py) and [image_process.py](https://github.com/neurodata/brainlit/tree/develop/brainlit/preprocessing/image_process.py), along with tests in [test_preprocess.py](https://github.com/neurodata/brainlit/tree/develop/tests/archive/test_preprocess.py) and [test_image_processs.py](https://github.com/neurodata/brainlit/tree/develop/tests/archive/test_image_process.py). This means: - [ ] typing hints on every method and class - [ ] google-formatted...