Kevin Mader kmader

kmader / README.md

Last active March 15, 2021 13:25 — forked from bellbind/loader.html

[threejs][html5]STL File Viewer with HTML5 File API

You can generate (binary) STL files from

kmader / CellWorkflow.zip

Last active August 29, 2015 14:20 — forked from kmader/batchimage.condor

The basic condor setup for a job processing a simple cell image using KNIME

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kmader / A ImageJ Analysis.ijm

Last active August 29, 2015 14:01 — forked from kmader/A analysis.ijm

Code for Birkedal to do slice by slice analysis

	// 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 / batchimage.condor

Last active August 29, 2015 14:01 — forked from kmader/mandelbrot.condor

A condor script for filtering and thresholding a given image using a number of different parameters

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


	universe = vanilla
	getenv = True # MATLAB needs local environment

kmader / ellipsoid_analysis.m

Last active August 29, 2015 14:00 — forked from kmader/Matlab Shape Analysis Function

A full shape analysis for 3D images segmented in matlab in the format used by bwlabeln or watershed

	% 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(:));