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BlueBrain / NeuroM

Neuronal Morphology Analysis Tool
https://neurom.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Find apical point in a tree #271

Closed lidakanari closed 3 years ago

lidakanari commented 8 years ago

This property is needed for many tasks (synthesizer, morphology release, classification of neurons, validation). The best approximation so far is the function available in Pneumatk, but it still does not give 100% correct results. Could we include this functionality in NeuroM?

eleftherioszisis commented 8 years ago

Yes, I think that would be important to be included in NeuroM. If this algorithm is the best we can do to estimate this point by taking into account only the morphometrics of a cell (i.e. without electrical behavior), then we should use it.

juanchopanza commented 8 years ago

Do we have a clear description of an algorithm to do this, and that it means for results to be "correct" or not?

lidakanari commented 8 years ago

I could write up a scheme of the current algorithm that is used to find the apical point. The problem is we don't have a clear description of the definition of the apical point (from biology). So your second point is practically what we are missing.

chalimou commented 7 years ago

It is crucial for the validation of the apical dendrites of the pyramidal cells to be able to extract the morphometrics of the apical tuft and the obliques separately, like section lengths, bifurcation angles, path distances etc.

mgeplf commented 7 years ago

I have an example in this pull request: https://github.com/BlueBrain/NeuroM/pull/636

Let me know if that helps.

asanin-epfl commented 3 years ago

Closing as the issue have been resolved via #636. See https://github.com/BlueBrain/morph-tool/blob/master/morph_tool/apical_point.py for details.