To do...
Figure: Visualization of soma detection pipeline. See "Inference" section for description of each step.
Add code block that shows how to run code...
Add image of what the code prints out...
The objective of this step is to generate initial proposals for potential soma locations by detecting blob-like structures in the image. Our proposal generation algorithm consists the following steps:
a. Smooth image with Gaussian filter to reduce false positives.
b. Laplacian of Gaussian (LoG) to enhance regions where the gradient changes rapidly, then apply a non-linear maximum filter.
c. Generate initial set of proposals by detecting local maximas.
d. Shift each proposal to the brightest voxel in its neighborhood. If the brightness is below a threshold, reject the proposal.
Figure: Example of proposals generated across a large region.
To do...
To do...
To do...
To use the software, in the root directory, run
pip install -e .