add neuron volume and taper analysis

carshadi commented 5 years ago

carshadi commented 5 years ago

This pull request adds compartment volume analysis as well as mean burke taper vs. branch order

tferr commented 5 years ago

Welcome to the SNT community @carshadi! Thanks for your contribution. This is great!

A couple of comments:

[ ] It would be important to add references to the formulas used, and which assumptions/approximations are made on volume calculation
[ ] Also important is to compare the results against L-measure (or btmorph?) to ensure the accuracy of the result. The simplest way would perhaps to load a neuron (with traced diameters) from http://neuromorpho.org/, since metrics of neuromorpho cells are already online
[ ] Add some sanity checks warning users analyzing reconstructions without/(or constant) diameter
[ ] ij.gui.plot is the only ij1 legacy library that you are using. The IJ2 alternative is PlotService. I am not sure if the API is already public, if it is, it would be nice to include it.
[ ] Why not include Hillman taper? Do you agree? Do you need snippets for the above? Also, Is there anything else you would like to be reviewed?

Thanks once more for your contribution!

tferr commented 5 years ago

Hi @carshadi, really sorry it took so long to come back to this. It is just that I was trying to tidy the scripting API, and wanted things to be settled before merging this. I had some minor comments on changes that need to be done so that it can run on the current API. If you don't have the time, let me know and I'll do them, I just thought you would like to do them yourself. Also, we probably would need to change the script to the Analysis folder so it is listed in the right submenu in the Script Editor, and we would need to rename it to something more descriptive. Any ideas?

Also, is there any way to incorporate to write a jython version of that numpy code you had on the convex hull? that would be a killer addition! I guess there would be three options for it: 1) Make this script export tagged SWC nodes (like the JWS) and paste at the bottom the native python code, so that users can run it with native Python elsewhere 2) Port this script to a Python notebook using the Scijava-jupyter-kernel: This would allow using NumPy, SciPy, OpenCV, etc. To do this have a look at the examples in the tutorials repository 3) Write a jython function from scratch that computes the convex hull so that the script becomes self-contained Option 2 would be my preferred: It would be truly transformative to the field to have a neuroanatomy package with direct access to both the ImageJ and Python ecosystems.

carshadi commented 5 years ago

I mistakenly created a new pull request reflecting the requested changes instead of updating to this one. Possibly because I did not have GitKraken setup when creating the initial PR. New pull request here https://github.com/fiji/Simple_Neurite_Tracer/pull/42

tferr commented 5 years ago

No problem! Thanks a lot! For future ref, this was superseded by #42 that meanwhile has been merged

fiji / SNT

add neuron volume and taper analysis #40