Hello and thank you.
Yes that is the exact part of the documentation to which I was referring.
Okay I am new here and so sorry if this is bad forum etiquette, but I’ll try and be as detailed as possible in case you can spot any obvious mistakes I am making!
This is my macro, that I type into process–> batch → macros
run("Set Scale...", "distance=2.1658 known=1 pixel=1.000 unit=micron global");*
run("Convert to Mask");*
run("Sholl Analysis (From Image)...", "startradius=5.0 stepsize=5.0 endradius=150.0 hemishellchoice=[None. Use full shells] previewshells=false nspans=3.0 nspansintchoice=Mean primarybrancheschoice=[Infer from starting radius] primarybranches=0.0 polynomialchoice=['Best fitting' degree] polynomialdegree=0.0 normalizationmethoddescription=Semi-Log normalizerdescription=Default plotoutputdescription=[None. Show no plots] tableoutputdescription=[Detailed table] annotationsdescription=[ROIs (points and 2D shells)] lutchoice=mpl-viridis.lut luttable=net.imglib2.display.ColorTable8@47fe0007 save=true savedir=[**my desired folder**] analysisaction=[Analyze image]");
If I process, FIJI just gets stuck on an empty Sholl Analysis 3.2.0 dialog box. Weird.
So I went back to try and debug using just one image at a time. Problems that I encounter with this are:
- It won’t accept end radius as NaN like your documentation says you can do, for images of different sizes. I can overcome this by making an overly large end radius.
- It does not recognise the point I previously (using step 5 of the documentation) as an ROI
- If I manually make a new ROI and press analyze image, I get error message: "IO FAILURE: Some file(s) (1/2) could not be saved. Please ensure “Destination” directory is valid. " - It is successfully saving the Sholl Profile linear plot, and the .csv Sholl profiles, it is not saving the ROIs (points and 2D shells)
Sorry, this feels like a lot and I understand if you can’t help me, the main worry is that I have to manually trace all my cells again so it’s good you said I shouldn’t need to do that!
Thanks so much,