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Hi All,
We have a slide-scanner which images sequentially across a tissue section and then creates a large composite tiled image. We can output the files as individual tiles as well in RAW format. However, I am attempting to assist a few students who have deleted the individual tile files and now want to divide their images into individual tiles (e.g.512 x 512 pixels) for the analysis. So what we need to do is divide the large image into separate tiles and output them as an image sequence. I thought I could do it by creating rectangles and cropping or duplicating but can't work out how to get it working across the entire image. Can anyone help me with this? I'm starting to think it might be easier to rescan the sections and get the raw data again! 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 |
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The opensource BioImage Convert may do this since it handles a variety of
file types: http://bioimage.ucsb.edu/downloads/BioImage%20Convert They have executables for Windows, Mac, and Linux. An example from their website for making tiles is: imgcnv -i MY_INPUT_IMAGE.jpg -o MY_OUT_FOLDER/MY_OUT_BASE_NAME.jpg -t jpeg -tile 256 Alternatively, there's a powerful Python script "tilemaker.py" that is easily modified for special tasks. http://code.google.com/p/panojs/source/browse/trunk/scripts/tilemaker.py?r=2 although it handles a more limited set of file types supported by the Python PIL library. On Thu, Oct 11, 2012 at 1:22 AM, Jacqui Ross <[hidden email]>wrote: > Hi All, > > We have a slide-scanner which images sequentially across a tissue section > and then creates a large composite tiled image. We can output the files as > individual tiles as well in RAW format. > > However, I am attempting to assist a few students who have deleted the > individual tile files and now want to divide their images into individual > tiles (e.g.512 x 512 pixels) for the analysis. > > So what we need to do is divide the large image into separate tiles and > output them as an image sequence. > > I thought I could do it by creating rectangles and cropping or duplicating > but can't work out how to get it working across the entire image. Can > anyone help me with this? > > I'm starting to think it might be easier to rescan the sections and get > the raw data again! > > 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 > > -- > John Kielkopf > Professor of Physics and Astronomy > University of Louisville > Louisville, KY 40292 > Tel:502.852.5990 > Fax:502.852.0742 > > > > <http://imagej.nih.gov/ij/list.html> ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Jacqueline Ross
Hi Jacqui,
On Thu, 11 Oct 2012, Jacqui Ross wrote: > So what we need to do is divide the large image into separate tiles and > output them as an image sequence. You might want to start from this macro: -- snip -- run("Clown (14K)"); tileWidth = 32; tileHeight = 19; setBatchMode(true); original = getImageID(); width = getWidth(); height = getHeight(); stack = 0; // the ID of the output; will be created on demand for (x = 0; x < width; x += tileWidth) { currentTileWidth = width - x; if (currentTileWidth > tileWidth) currentTileWidth = tileWidth; for (y = 0; y < height; y += tileHeight) { currentTileHeight = height - y; if (currentTileHeight > tileHeight) currentTileHeight = tileHeight; // copy the tile selectImage(original); makeRectangle(x, y, currentTileWidth, currentTileHeight); run("Copy"); run("Select None"); if (stack == 0) { newImage("Tiled " + getTitle(), "RGB", tileWidth, tileHeight, 1); stack = getImageID(); } else { selectImage(stack); run("Add Slice"); } makeRectangle(0, 0, currentTileWidth, currentTileHeight); run("Paste"); setMetadata("Label", "(x=" + x + ",y=" + y + ")"); } } if (stack != 0) { selectImage(stack); run("Select None"); setSlice(1); // work around bug: the slider is at slice 1, // but the last slice is shown } setBatchMode(false); -- snap -- Use either Fiji's script editor (File>New>Script, followed by Language>ImageJ Macro) or the bare-bones editor of ImageJ 1.x (Plugins>New>Macro), paste the code and modify it to your liking (you might want to remove the line opening the clown sample, adjust the image type of the new type or replace newImage() with a call to the Duplicate... plugin, and maybe adjust the slice label format). Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Jacqueline Ross
Hi Jacqui,
Jacqui Ross wrote: > Hi All, > > We have a slide-scanner which images sequentially across a tissue section and then creates a large composite tiled image. We can output the files as individual tiles as well in RAW format. > > However, I am attempting to assist a few students who have deleted the individual tile files and now want to divide their images into individual tiles (e.g.512 x 512 pixels) for the analysis. > > So what we need to do is divide the large image into separate tiles and output them as an image sequence. > > I thought I could do it by creating rectangles and cropping or duplicating but can't work out how to get it working across the entire image. Can anyone help me with this? > > I'm starting to think it might be easier to rescan the sections and get the raw data again! > > 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 > ... [show rest of quote] If you're not into writing a macro or script, you can use the in built
function 'Image>Stack>Tools>Montage to stack...' which lets you choose how many rows and columns you want your large image split, leave border width at 0 and you get a stack of your tiles that you can save as image sequence. Christian -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Jacqueline Ross
Hi Jacqui,
> So what we need to do is divide the large image into separate tiles and > output them as an image sequence. You can also do this using the Bio-Formats command line tools: http://loci.wisc.edu/bio-formats/command-line-tools You would use a series of calls to the "bfconvert" command line tool with the "-crop" option to create tiles sized to your liking; e.g., "-crop 0,0,512,512", "-crop 512,0,512,512", etc., up to the size of your planes in 2 dimensions. Regards, Curtis On Thu, Oct 11, 2012 at 12:22 AM, Jacqui Ross <[hidden email]>wrote: > Hi All, > > We have a slide-scanner which images sequentially across a tissue section > and then creates a large composite tiled image. We can output the files as > individual tiles as well in RAW format. > > However, I am attempting to assist a few students who have deleted the > individual tile files and now want to divide their images into individual > tiles (e.g.512 x 512 pixels) for the analysis. > > So what we need to do is divide the large image into separate tiles and > output them as an image sequence. > > I thought I could do it by creating rectangles and cropping or duplicating > but can't work out how to get it working across the entire image. Can > anyone help me with this? > > I'm starting to think it might be easier to rescan the sections and get > the raw data again! > > 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 > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Curtis, Christian, Johannes & John,
Thanks very much to each of you for your suggestions. The easiest method is the one suggested by Christian so I think the students can use that method since it doesn't really matter if the tiles are a certain size. I haven't yet managed to get the other methods working properly but haven't had much time this week to pursue them properly. I hope it's OK to come back to you if I have further questions. Thanks! 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/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Friday, 12 October 2012 6:10 a.m. To: [hidden email] Subject: Re: Creating individual tiles from one large image Hi Jacqui, > So what we need to do is divide the large image into separate tiles > and output them as an image sequence. You can also do this using the Bio-Formats command line tools: http://loci.wisc.edu/bio-formats/command-line-tools You would use a series of calls to the "bfconvert" command line tool with the "-crop" option to create tiles sized to your liking; e.g., "-crop 0,0,512,512", "-crop 512,0,512,512", etc., up to the size of your planes in 2 dimensions. Regards, Curtis On Thu, Oct 11, 2012 at 12:22 AM, Jacqui Ross <[hidden email]>wrote: > Hi All, > > We have a slide-scanner which images sequentially across a tissue > section and then creates a large composite tiled image. We can output > the files as individual tiles as well in RAW format. > > However, I am attempting to assist a few students who have deleted the > individual tile files and now want to divide their images into > individual tiles (e.g.512 x 512 pixels) for the analysis. > > So what we need to do is divide the large image into separate tiles > and output them as an image sequence. > > I thought I could do it by creating rectangles and cropping or > duplicating but can't work out how to get it working across the entire > image. Can anyone help me with this? > > I'm starting to think it might be easier to rescan the sections and > get the raw data again! > > 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 > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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