kmader

% this function (will) performs the ellipsoid based shape analysis on a 3D image
% the input is a labeled image probably from the bwlabel function
% the output is an array formatted like such
% labelId, volume, centerX, centerY, centerZ, extentsX, extentsY, extentsZ, pca1X, pca1Y, pca1Z, score1, score2, score3
function [out_table]=ellipsoid_analysis(in_image,out_file)
% create an array the same size as the image of x,y, and z points. This way we can calculate
% center of volume and other parameters by using multiplication
[xgrid,ygrid,zgrid]=meshgrid(1:size(in_image,1),1:size(in_image,2),1:size(in_image,3));

num_of_obj=max(in_image(:));

kmader

##################################################################
##
## Run a parameter sweep with threshold and filter using condor
##	Filename: batchimage.condor
##
##################################################################


universe	= vanilla
getenv		= True		# MATLAB needs local environment

kmader

// taken from https://gist.github.com/kmader/10871528
// Load the data in
imageStackDirectory=getDirectory("Select the folder where the images should loaded from");
run("Image Sequence...", "open="+imageStackDirectory+" sort use");
// crop the image
makeRectangle(1089, 993, 675, 702);
run("Crop");
// clear the meaningless pixel sizes and set them to 0
run("Properties...", "unit=pixel pixel_width=1 pixel_height=1 voxel_depth=1 global");
// set which metrics to record for each analysis

kmader

kmader

demo: https://rawgit.com/kmader/ccabb1b4ded4bf1bc47994c22ff60a6d/raw/loader.html

You can generate (binary) STL files from

https://rawgit.com/bellbind/5eb1bb3cd94371973f45/raw/geom.html