Provide statistical output

fiji / SNT

Legacy project superseded by https://github.com/morphonets/SNT

GNU General Public License v3.0

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Provide statistical output #10

Closed tferr closed 6 years ago

tferr commented 7 years ago

Right now the ability to summarize reconstructions statistically is rather poor and limited to the the Export as csv command or the Analyze Skeleton output that runs on digitized paths. There is really no straight forward way to obtain at a glance things such as N. of branch points, Total length, etc... Otherwise, we should at least point users to web-tools such as L-measure or Remod or nat

tferr commented 7 years ago

A list of external tools is being compiled at https://imagej.net/Neuroanatomy:External_Resources. . There is also lots of Python code for visualization and analysis that ought to be added to this list. E.g.,

BlenderSWCVizualizer: https://github.com/dEvasEnApati/BlenderSWCVizualizer
NeuroM: https://github.com/BlueBrain/NeuroM
btmorph_v2: https://github.com/btorboist/btmorph_v2

It would be really nice to generate some Jupyter Notebooks (see also huangziwei/TracePy#1). But perhaps such effort already started elsewhere? @dEvasEnApati, @btorboist, @huangziwei, @BlueBrain, any thoughts?

tferr commented 6 years ago

Just for those monitoring this issue: Without any feedback just went ahead and wrote a couple of scijava commands. It is now possible to:

Measure filtered paths
Retrieve summary statistics (with distribution histograms) of common properties
Perform Strahler analysis Here is how it looks:

I'm closing this now, but I still think it would be great generate some Jupyter Notebooks. Will reopen if someone gets interested in this again