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reconstrue / brightfield

Reconstruction of biocytin-stained neurons detected in brightfield microscopy image stacks
http://reconstrue.com
Apache License 2.0
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Neuroglancer plus Tensorflow.js #86

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

Tigue on twitter noticing that neuroglancer has tensorflow.js as a dep.

Since neuroglancer can generate non-ortogonal planes, users can navigate to a good perspective and then run a MinIP style tracing on 2D then projecting to 3D trick.

Since the scene doesn't change, multiple runs of auto-tracer from different camera vectors can accumulate their probability maps. So, user can nav around until probabilities in an area are high enough and then move on. So, probabilities are another layer (so that user can know where more work needs to be done b/c probabilities are low).

JohnTigue commented 4 years ago

Looks like this is the code to start with. Clearly someone is mixing neuroglancer and tfjs, for some purpose:

https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/computed/tensorflow

JohnTigue commented 4 years ago

So, Tensorflow server-side with Tesla T4 GPU for transfer learning based training. Then download model to Tensorflow.js in-browser for inference live in Neuroglancer using the client-side GPU. Colorize voxels according to a classifier's inferred probability.