I’m trying automate analysis of tracings made in simple neurite tracer using sholl analysis(Analysis ▷ Sholl ▷ Sholl Analysis (Tracings)…). I’ve tried following the Sholl Analysis wiki but can’t figure it out. When I record a macro for the Sholl Analysis (Tracings) plugin I get this code:
run("Sholl Analysis (Tracings)...", "traces/(e)swc=[/Volumes/EZ Ext HD1/Quantification/^CSPG Coating Quant/98137 trace & sholl/B2-1-1//B2-1.50CSPG+RM.CS56.traces] image=[/Volumes/EZ Ext HD1/Quantification/^CSPG Coating Quant/98137 trace & sholl/B2-1-1//B2-1.50CSPG+RM.CS56.tif] center=[Center of soma] radius=1 enclosing=1 #_primary=1 infer linear polynomial=[Best fitting degree] most normalizer=Area/Volume show save directory=[/Volumes/Macintosh HD/Users/X/Desktop]"); selectWindow("Sholl profile (Log-log) for B2-1.50CSPG+RM.CS56.traces no-filtering (407.522,482.246,0.000)");
I’m wondering how I can make my life easier by making the file directory a generic one so I can just plug in files and not have to click all the options for each individual trace. Or even better, I would like to batch process this but that seems difficult with .tracings files.