brainlit
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neurodata
Method container for computational neuroscience on brains.
Neuron trace coordinates typically come in one of two coordinate systems: physical (e.g. microns) or voxel (e.g. coordinates relative to corner of image, in units of voxels). Cloudvolume handles this...
running pytests raises various warnings (e.g. ndimage.morphology is deprecated), lets update the code to solve these warnings.
Pytorch 3D CNN model architecture for training on 3D voxels. Easily editable example notebook (found in experiments -> pytorch_model) illustrates the model's application on the 50 image Mouselight benchmarking data....
It would be great to uncomment the test [here](https://github.com/neurodata/brainlit/blob/develop/brainlit/napari_viterbrain/tests/test_plugin.py)
I tested two trivial PR's, one from a [fork](https://github.com/neurodata/brainlit/pull/341) where I got an AWS error, and one from a [branch](https://github.com/neurodata/brainlit/pull/342) where there was no error. Is it possible to allow...
For my senior project: I would like to program a way to take a binary neuron image and convert it to a swc trace automatically. Includes: performing experiments (including mapping...
tutorial [here](https://circleci.com/docs/2.0/parallelism-faster-jobs/) i started a pr [here](https://github.com/neurodata/brainlit/pull/328), but the tests still need to be split across the different containers. Currently (I believe) all 4 containers are running all the tests.
There is a function that, given a component in a segmentation, computes the bounding box with a certain padding ([here](https://github.com/neurodata/brainlit/blob/bc4e388485dbf6cbf0933dbf01e3b4299794e564/brainlit/algorithms/connect_fragments/dynamic_programming_viterbi2.py#L249)). However this can be simplified by utilizing the [regionprops](https://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops) method...