brainlit

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combine applying ilastik

1

[this](https://github.com/neurodata/brainlit/blob/develop/brainlit/BrainLine/apply_ilastik.py) and [this](https://github.com/neurodata/brainlit/blob/develop/brainlit/algorithms/generate_fragments/state_generation.py) both apply ilastik in parallel, can they be combined?

tathey1

replace NeuronTrace with nGauge?

1

Maybe we use [nGauge](https://github.com/Cai-Lab-at-University-of-Michigan/nGauge) instead of [NeuronTrace](https://github.com/neurodata/brainlit/blob/develop/brainlit/utils/Neuron_trace.py)? It seems concise+efficient (it was published), works with blender, plus other people use it.

tathey1

add instructions on labeling validation data to brainline

1

tathey1

only run segmentation on chunks that have brain tissue

2

currently, i run the segmenter on the whole volume

tathey1