brainlit
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neurodata
Method container for computational neuroscience on brains.
We forward the netlify documentation website to neurodata.io and somewhere along the way it becomes insecure. Everything looks good on the netlify end.
[Issue #166](https://github.com/neurodata/brainlit/issues/166) suggests converting [swc.py](https://github.com/neurodata/brainlit/issues/166) into a Neuron Trace class with getter methods utilizing functions in swc.py. What sorts of features would be ideal for this class?
Matlab dominates python in image interpolation. It may be possible to use the appropriate MEX file in MATLAB copy matlab's interpolation code and create a Cython file for python which...
[Here ](https://link.springer.com/article/10.1007/s12021-018-9407-8) is a paper with an interesting approach to neuron reconstruction. To what extent can it be used/is it effective on our data?
Something along the lines of the functino napari_viewer in [this file](https://github.com/neurodata/mouselight_code/blob/tom/connect_fragments/mouselight_code/src/visualize.py). Input should include images, labels, points, and shapes objects, and this wrapper will call the appropriate napari functions to...
Code here: https://github.com/microsoft/InnerEye-DeepLearning Make it possible to run an experiment like that here: https://neurodata.io/talks/mouselight/TTA2_Athey_Thomas_pdf.pdf This is very open-ended: almost any experiment/integration would be useful. Notes: -InnerEye is an example of...
Whenever we are checking on types ([example ](https://github.com/neurodata/brainlit/blob/20b08404a93b06f1b70f134987004445de67b515/brainlit/utils/session.py#L155)), we use the native Python int/float, but that means our functions reject all other related types, such as numpy or tensor floats....
DeepNeuron is a deep learning based algorithm for neuron reconstruction. Paper is [here](https://link.springer.com/article/10.1186/s40708-018-0081-2). Does it work well on our data?
- List installation steps - List tutorial steps - List common issues during this process and fixes
Merge python3.7-experimental branch into documentation branch for Windows users. Then windows users can use python3.7 to download data and finish the tutorial notebook for installation.
