Skip to content, Skip to search

Changes

Sholl Analysis

341 bytes added, 12:19, 19 October 2016
Add API example
Note that the IJM built-in [http://imagej.nih.gov/ij/developer/macro/functions.html#call call("class.method")] function can only pass strings to Java methods. For this reason, you have to quote the passed argument. <tt>Sholl_Analysis</tt> will then parse the string argument and interpreter its value. Note that calls made by the IJ macro language need to be set before running the plugin and remain in effect while ImageJ is running.
;Python example: Display only the main ''[[#Metrics|Sholl Table]]'', ignoring remaining outputs3D analysis of an image stack
<source lang="python">
#@ImagePlus imp#@LogService log from sholl import sholl.Option Sholl_Analysis, Options as sosoxc, yc, zc = 100, 100, 10 # x,y,z coordinates of centerdistances = [10,20,30,40,50] # sampling radiilowerT, upperT = 100, 255 # threshold values sa = Sholl_Analysis()sa.setThreshold(lowerT, upperT) sa.setCenter(xc, yc, zc) log.info("Analyzing "+ imp.getTitle())profile = sa.setNoPlotsanalyze3D(Truexc, yc, zc, distances, imp) # Exclude plots from outputsofor idx, inters in enumerate(profile): log.setNoTableinfo("r=" + str(distances[idx]) +": "+ str(Trueinters) # Exclude detailed table from output+" intersections")  
</source>
;Java/BeanShell/Groovy example: Display plots without annotations
Emailconfirmed
1,643
edits