README

Deep-Learning-Based Neuron Detection in Whole-Brain Volumes

The three scripts in this directory test Prerna Singh's 3D-CNN on three different datasets from Brain 1:
  • compareSubvols.ipynb: The middle-most volume within the brain (1020x1020x1020 voxels)

  • testJacoData.ipynb : 174 subvolumes (from Jaco's experiment) that contain all 180 known cells

  • wholeBrain.ipynb : The entire Brain 1 dataset

Before reproducing this experiment, make sure that:

This experiment does not require a GPU (CUDA is not needed for PyTorch), but it would help it run faster.

If you are using conda, make sure that both brainlit and PyTorch are installed within the same environment.