README¶
Manuscript¶
Athey, T. L., Tward, D. J., Mueller, U., & Miller, M. I. (2021). Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction. arXiv preprint arXiv:2106.02701.
How to use ViterBrain¶
First, make sure that you have installed the
brainlit
package [Documentation].Second, uncompress the data
brainlit/experiments/ViterBrain/data/example.zip
.- Then, you can run some of the tutorial notebooks in the
notebooks
folder: ViterBrain.ipynb
- shows a programmatic example of the pipeline, based on zarr inputs.fig3-voxels.ipynb
- generates Figure 3 from the paper.fig7-results.ipynb
- generates Figure 7 from the paper.other notebooks can be useful for referemce, they were used in generating results in the paper.
- Then, you can run some of the tutorial notebooks in the
- The files in the
scripts
folder also can be useful: napari_gui.py
- shows the GUI prototype.click on colored fragment to select, red arrow will identify orientation.
o-key to switch orientation of selected fragment.
click on another colored fragment (and hit o-key if necessary to switch orientation).
click no the labels layer in the left hand pane, then click somewhere on the image (not on a fragment)
t-key to trace between fragments.
c-key to clear the selected fragments.
q-key to clear all annotations.
n-key to change colors (3 total colors).
other scripts are for reference for benchmarking the timing of the pipeline.
- The files in the