http://imagej.273.s1.nabble.com/Creating-individual-tiles-from-large-montage-file-tp5016947p5016952.html
I couldn't resist checking my email again tonight to see if you had a solution for me! Thank you so much for this. It is working absolutely brilliantly.
It also helps me to understand the syntax better as I can see now what I was doing wrong and I'll be able to use this code for other macros too. I'm sure it will also be helpful to others.
run("Image Sequence... ", "format=TIFF name=["+ imgName +"] start=0
> Thanks Jerome,
>
> I can now get the correct naming! The extension is still there as part of
> the name but that doesn't matter.
>
> I'd like to have the files going into a specified Destination folder, dir2
> so that it's a bit more generic.
>
> How would I add in that step?
>
> I've used the code below before for saving individual files into folders
> but not for a sequence;
>
> saveAs("TIFF", dir2 + title);
> close();
>
> }
>
> So, I’m assuming I can somehow adapt this...?
>
> Cheers,
>
> Jacqui
>
> Jacqueline Ross
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Tel: 64 9 923 7438
> Fax: 64 9 373 7484
>
>
http://www.fmhs.auckland.ac.nz/sms/biru/>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Jerome Mutterer
> Sent: Friday, 29 July 2016 7:19 p.m.
> To:
[hidden email]
> Subject: Re: Creating individual tiles from large montage file
>
> Dear Jacqui,
> the getTilte() function works as expected, but because you have spaces in
> the tilte, you should add square brackets in the "Image Sequence..."
> command arguments. You can also specify the output folder using the save
> parameter, like this:
>
> run("Image Sequence... ", "format=TIFF name=["+ imgName +"] start=0
> digits=4
> save=/Users/jmutterer/Desktop/aaa");
>
> Sincerely,
>
> Jerome
>
>
> On 29 July 2016 at 09:05, Jacqui Ross <
[hidden email]> wrote:
>
> > Dear All,
> >
> > We have a system that creates very large stitched images from individual
> > raw data files. I'm helping one of our graduate students to do some image
> > analysis and unfortunately her files are far too large to be able to
> > process the stitched image and she has somehow forgotten to copy and
> store
> > safely the raw data, which we often use for the analysis.
> >
> > So, I would like to create a macro that will cut these large images into
> > tiles of a size that can be managed, i.e. reverse the process.
> >
> > I've made some progress but have two issues. One is that her file names
> > have spaces in them. When I use the ImgName=getTitle() command, it seems
> to
> > cut off the title at the space. Is there another command that can be used
> > that will get the full name including spaces? If not, is there an easy
> way
> > to rename these images with underscore or hyphens in place of spaces as a
> > first step?
> >
> > The second problem is that instead of saving the image stack
> automatically
> > as a sequence, it's asking me to confirm the file name. It might just be
> > that it's late on a Friday afternoon (for me) but I can't work out what
> > I've done wrong.
> >
> > I've copied the macro below and I would very much appreciate some help !
> > I've also attached it as a text file in case something goes wrong with
> the
> > lines..
> >
> >
> > //This macro splits a stitched image into 5 x 5 individual tiles and
> saves
> > as a sequence into a Destination folder
> > dir1 = getDirectory("Choose Source Directory ");
> > dir2 = getDirectory("Choose Destination Directory ");
> > list = getFileList(dir1);
> > setBatchMode(true);
> > for (i=0; i<list.length; i++) {
> > showProgress(i+1, list.length);
> > open(dir1+list[i]);
> > imgName=getTitle();
> > run("Montage to Stack...", "images_per_row=5 images_per_column=5
> > border=0");
> > run("Image Sequence... ", "format=TIFF name="+imgName+"start=0
> digits=3");
> > close();
> >
> > }
> >
> > Kind regards,
> >
> > Jacqui
> >
> > Jacqueline Ross
> > Biomedical Imaging Microscopist
> > Biomedical Imaging Research Unit
> > School of Medical Sciences
> > Faculty of Medical & Health Sciences
> > The University of Auckland
> > Private Bag 92019
> > Auckland 1142, NEW ZEALAND
> >
> > Tel: 64 9 923 7438
> > Fax: 64 9 373 7484
> >
> >
http://www.fmhs.auckland.ac.nz/sms/biru/> >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
>
>
> --
> Jerome Mutterer
> CNRS - Institut de biologie moléculaire des plantes
> 12, rue du Général Zimmer
> 67084 Strasbourg Cedex
> www.ibmp.cnrs.fr
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>