Thomas Athey

> @jni You can found the code on (License MIT) > https://github.com/DMST1990/Skeletonization > with some examples, (a few unit tests) and documentation. > The code structure is quite different to...

here: https://github.com/neurodata/brainlit/blob/tathey1-ailey/experiments/deisseroth/axon_loop_vols.py

great, i think that maybe we should remove it from Neuron_trace, and make sure that we switch every time it is called to the version in trace_evaluation. What do you...

spatial distance is described in methods [here](https://www.nature.com/articles/nbt.1612)

@Swarnlataaa thanks for your interest in this issue. I'm mostly thinking about the classes `ApplyIlastik` and `ApplyIlastik_LargeImage` [here](https://github.com/neurodata/brainlit/blob/develop/brainlit/BrainLine/apply_ilastik.py). It would be great if analagous arguments/attributes are the same across these...

Some of these warnings might be easy to fix, some might be hard. Maybe you can make some quick notes on the warnings that occur to see if any of...

Things have updated since I posted this so the function in question is [here](https://github.com/neurodata/brainlit/blob/1960fd8d8d740b434c061e9fb366f56ded47106a/brainlit/algorithms/generate_fragments/state_generation.py#L533) now. It would be good to sketch out (like on paper) what the change would involve....

@ahillsley which python version worked for you? I got the same longinterpr.h error in 3.12, and got the following errors in 3.9.5 and 3.9.6: ``` waterz/evaluate.cpp:3429:41: error: no member named...