## 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.

• 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.