Batch Stack Focusing
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Batch Stack Focusing
 
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Re: Batch Stack Focusing
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Re: Batch Stack Focusing
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Re: Batch Stack Focusing
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Re: Batch Stack Focusing
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Dear Kees,
Many thanks for your help! I have edited my code according to your suggestion but I still don't see any stacked images being saved.
When I supplement the processfile(path) function to subtract the background of all the images, it does not that no problem. Perhaps the issue relates to the fact I'm trying to process each sequence of images within a single subfolder and not all the images at once?
Any other suggestions would be greatly appreciated!
Kind regards,
Amy From: Straatman, Kees (Dr.) [via ImageJ] <ml-node+[hidden email]>
Sent: 01 April 2017 12:58 To: AC17 Subject: Re: Batch Stack Focusing Dear Amy,
You don't give a directory where to save the files. Your " saveAs("Tiff", "stack" );" should read something like ' saveAs("Tiff", dir2+"stack" );' After the line " dir = getDirectory("Choose image sequence folder");" you can add a line 'dir 2= getDirectory("Choose folder to save results");' and of course you have to give the argument dir2 also to the correct function. If you want to save the results in the original directory you can just use saveAs("Tiff", dir+"stack" ); Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging Facility Centre for Core Biotechnology Services University of Leicester http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif ImageJ workhops 1 and 2 June: http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/workshops/imagej-workshops-June-2017
-----Original Message----- From: AC17 [mailto:[hidden email]] Sent: 31 March 2017 17:27 To: [hidden email] Subject: Re: Batch Stack Focusing Hello Daan, Thank you for your reply! I changed my code based on your recommendations but it still doesn't seem to be working. Some processing is happening and I don't receive any error messages but I don't see any files saved. Can you suggest anything else I could try? Many thanks, Amy ________________________________ From: Daan VAN DEN BRINK [via ImageJ] <[hidden email]> Sent: 28 March 2017 16:03 To: AC17 Subject: Re: Batch Stack Focusing Hello Amy, I had a super quick look at your macro. Could it be that the closing bracket of the for-loop in the 'processFile(path)' function is not enclosing all the commands? Also, all you files will be named "stack". Hope that helps. Daan On 27/03/17 14:08, AC17 wrote: > Hi all, > > This is my first time attempting to write a macro in image J. I would > really appreciate your help with this… > > I have a main directory with multiple subdirectories. Each > subdirectory contains multiple images (z stacks). I would like to > write a code which will take my main directory and open a subdirectory > , open all the images in that subdirectory, stack the images, run the > stack focusing plugin and then save the stack in the corresponding > folder. I would like to loop this so that all the subdirectories within my main directory are processed. > > This is what I have so far. This code runs for a few minutes but I > then can’t find my saved stacks. > > dir = getDirectory("Choose image sequence folder"); > setBatchMode(true); > count = 0; > countFiles(dir); > n = 0; > processFiles(dir); > print(count+" files processed"); > > function countFiles(dir) { > list = getFileList(dir); > for (i=0; i<list.length; i++) { > if (endsWith(list[i], "/")) > countFiles(""+dir+list[i]); > else > count++; > } > } > > function processFiles(dir) { > list = getFileList(dir); > for (i=0; i<list.length; i++) { > if (endsWith(list[i], "/")) > processFiles(""+dir+list[i]); > else { > showProgress(n++, count); > path = dir+list[i]; > processFile(path); > } > } > } > > function processFile(path) { > for (i=0; i<list.length; i++) > open(path);} > { > run("Images to Stack", "name=Stack title=[] use"); > run("Stack Focuser ", "enter=11"); > saveAs("Tiff", "stack" ); > close(); > } > > Many thanks for your help! > > Amy > > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Batch-Stack-Focusing-tp5018376.html imagej.1557.x6.nabble.com Batch Stack Focusing. Hi all, This is my first time attempting to write a macro in image J. I would really appreciate your help with this… I have a main directory with multiple subdirectories.... > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html ImageJ Mailing List - National Institutes of Health<http://imagej.nih.gov/ij/list.html> imagej.nih.gov home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers. -- *Daan M. VAN DEN BRINK* Laboratoire de Biologie et Modélisation de la Cellule (LBMC) - UMR 5239 Team Mollereau *ENS de Lyon* — Site MONOD - LR2 46 allée d'Italie — 69364 LYON CEDEX 07, FRANCE Tel.: +33 (0)4.72.72.89.29 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html ImageJ Mailing List - National Institutes of Health<http://imagej.nih.gov/ij/list.html> imagej.nih.gov home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers. ________________________________ If you reply to this email, your message will be added to the discussion below: http://imagej.1557.x6.nabble.com/Batch-Stack-Focusing-tp5018376p5018407.html ImageJ - Batch Stack Focusing<http://imagej.1557.x6.nabble.com/Batch-Stack-Focusing-tp5018376p5018407.html> imagej.1557.x6.nabble.com Batch Stack Focusing. Hi all, This is my first time attempting to write a macro in image J. I would really appreciate your help with this… I have a main directory with multiple subdirectories.... To unsubscribe from Batch Stack Focusing, click here< NAML<http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> -- View this message in context: http://imagej.1557.x6.nabble.com/Batch-Stack-Focusing-tp5018376p5018427.html Sent from the ImageJ mailing list archive at Nabble.com. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html If you reply to this email, your message will be added to the discussion below:
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Re: Batch Stack Focusing
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