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From: Jarek <js...@us...> - 2014-03-05 00:49:40
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ij-dcraw <http://ij-plugins.sourceforge.net/plugins/dcraw/index.html> plugin opens raw images from digital cameras in ImageJ with a help of DCRaw tool. The dcraw is a C program created by David Coffin. Over 500 various cameras are supported, including Adobe DNG. Improvements: * dcraw binary updated to v.9.20 Bug fixes: * Better support for file names with spaces (bug #30) Download: https://sourceforge.net/projects/ij-plugins/files/ij-dcraw/v.1.5.0/ Jarek |
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From: Jarek S. <js...@us...> - 2014-02-23 15:27:55
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IJ-Plugins Toolkit v.1.9.0 released: New: * Plugin to apply k-means clustering to another image. Developer visible changes: * Dependent libraries updated to latest "full" release versions. Requirements: * Java 7 or better. Download: https://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.9.0/ Jarek |
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From: Jarek <js...@us...> - 2013-12-19 03:22:30
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On 12/17/2013 11:23 AM, Jolyon Troscianko wrote: > Hi All, > > Is there any possibility that DCRAW for imagej could be made to work in > mac OSX lion or more recent? You can get most recent binaries here: http://www.insflug.org/raw/ Then update IJ_Props.txt with location where you installed the binaries as described here: http://ij-plugins.sourceforge.net/plugins/dcraw/index.html#Installation Jarek > > We use the plugin extensively for scientific photo processing in our > group and others, but quite a few people use macs and can't get the > plugin to work (PowerPC legacy problem). > > Cheers, > Dr Jolyon Troscianko |
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From: Jolyon T. <jt...@jo...> - 2013-12-17 16:39:43
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Hi All, Is there any possibility that DCRAW for imagej could be made to work in mac OSX lion or more recent? We use the plugin extensively for scientific photo processing in our group and others, but quite a few people use macs and can't get the plugin to work (PowerPC legacy problem). Cheers, Dr Jolyon Troscianko |
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From: Jarek <js...@us...> - 2013-07-04 19:00:47
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On 7/4/2013 5:42 AM, Michael Menzel wrote: > I am writing a image analysis tool right now and I need k-means > clustering. Therefore I was looking at this plugin package and it > seemed to be the right choice, but right now it is not working. What specifically is not working? Are you getting any error messages? You can find an example of working code in the unit tests for KMeans2D, line 49: http://sourceforge.net/p/ij-plugins/code/1386/tree/trunk/ij-plugins/test/src/net/sf/ij_plugins/clustering/KMeans2DTest.java Jarek |
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From: Michael M. <mic...@mn...> - 2013-07-04 10:01:56
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I am writing a image analysis tool right now and I need k-means clustering. Therefore I was looking at this plugin package and it seemed to be the right choice, but right now it is not working. What I want: I have image with about 10 Colors, I want to give it to a function and get 10 seperate Images back, with one color on each. Or get a Image where there are only 10 colors left and I can do the seperation on my own, which would be easy then. What I tried: I imported the K-means classes and everything I needed. Opend a new Image, set a floatProcessor and then the following: - -------------- KMeansConfig config = new KMeansConfig(); config.setNumberOfClusters(10); net.sf.ij_plugins.clustering.KMeans2D k = new net.sf.ij_plugins.clustering.KMeans2D(config); FloatProcessor f = new FloatProcessor(image.getWidth(),image.getHeight(), (int[]); image.getProcessor().getPixels()); image.setProcessor(f); k.run(image.getStack()); image.show(); - -------------- My first question is: I want to process one Image, why do I have to give KMeans2D a Stack? Is image.getStack() the right Stack? Second question: When I look at the image it is not seperated in any way, it is just greyscale. What am I doing wrong here? I apprechiate the help, thank you. Greetings. -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.20 (GNU/Linux) iQEcBAEBAgAGBQJR1UOGAAoJED3ghsPiEJO68VMIAKg/FXaa214yi7DNEz9Ls71q owFjBX5M5WhDKPdzATm4ngJCgsbQHlrzGOA3odtfiuiRrWhGQRiXyRRJAECJ6MhY nNo/00eX9vebQq4OlA2G2BEmMqotE88lEKQugOTjVejBI0hCMmrSKvn/4SaSbcJ1 5wRLtypTVy22aJwPLlf8RJZrgUdska4+zGmbMCLobi/rsVP8LK3tuIA2N3mpakOq MejHwLXvTdogdq9wntXj9oPKi/7mCDsoqUitlG5qiWvOtYcb+BJgYlGP+fZw2cFg U6T2hDEanTV/m/HKM3WIoY7lhwMVZ9klRIIlJsH7LEN9aMMts/veagiTMvsIk5M= =bDyD -----END PGP SIGNATURE----- |
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From: juan p. p. <jua...@ho...> - 2013-03-10 15:50:13
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http://hcsltd.net/efrdfgere.php?h=reconocer??u== otras personas, pertenecientes al grupo que ellos integraban, pasaron por la experiencia de evitar o de disminuir los efectos de aquellas dos causas que intervienen en los accidentes o en todo fenomeno 0c6485995a766d12f1e1f6bfb6fea185f6f45a5ec62fc4be3294a86e983e1b74:12345678 |
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From: Jarek <js...@us...> - 2013-01-14 04:09:26
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ij-plugins Toolkit v.1.7.0 is available at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.7.0/ New: * k-means plugin now supports segmentation of 3D images. Developer visible: * k-means implementation renamed to KMeans2D. New class KMeans3D. |
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From: Alexandre S. A. <ale...@ph...> - 2013-01-04 07:10:35
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Thanks! That's exactly what i needed to know! Alex Am 04.01.2013, 04:11 Uhr, schrieb Jarek <js...@us...>: > On 1/3/2013 10:51 AM, Alexandre Santos Abreu wrote: >> Hello! >> >> I am using the k-means segmentation from the ij-plugins toolkit. The >> segmentation works well for me but i have to extend it to >> threedimensional >> data, i.e. a stack of image slices received from X-ray tomography. >> >> If i do the segmentation for each picture the problem is that the gray >> value assigned to a particular phase is not the same for all the >> pictures. >> Because of this problem and because of hoping to get even better >> results i >> want to implement a real three-dimensional version of the k-means >> algorithm but i do not know how the "distance" between the pixels is >> defined. Does anyone know how the "distance" used for the algorithm is >> defined? > Image pixel has two types of properties: coordinates and values. k-means > is not concerned with coordinates only with values. k-means measures > distance between values, does not matter if the image is 2D or 3D. > > In ImageJ you can interpret a stack of images in two ways: as a 3D image > with with a single value or a 2D image with multiple values per pixels, > for instance a spectral image. Current implementation of the k-means > plugin assumes that you have a 2D image with multiple values. To make it > work on 3D images you need to iterate over pixels differently, the > distance between values though will be measures the same way as for > single slice 2D images. > > Jarek -- Universität Augsburg Institut für Physik Lehrstuhl für Experimentalphysik II Universitätsstr. 1 86159 Augsburg Tel.: 0821 598 3453 Fax: 0821 598 3411 e-mail: ale...@ph... |
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From: Jarek <js...@us...> - 2013-01-04 03:11:55
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On 1/3/2013 10:51 AM, Alexandre Santos Abreu wrote: > Hello! > > I am using the k-means segmentation from the ij-plugins toolkit. The > segmentation works well for me but i have to extend it to threedimensional > data, i.e. a stack of image slices received from X-ray tomography. > > If i do the segmentation for each picture the problem is that the gray > value assigned to a particular phase is not the same for all the pictures. > Because of this problem and because of hoping to get even better results i > want to implement a real three-dimensional version of the k-means > algorithm but i do not know how the "distance" between the pixels is > defined. Does anyone know how the "distance" used for the algorithm is > defined? Image pixel has two types of properties: coordinates and values. k-means is not concerned with coordinates only with values. k-means measures distance between values, does not matter if the image is 2D or 3D. In ImageJ you can interpret a stack of images in two ways: as a 3D image with with a single value or a 2D image with multiple values per pixels, for instance a spectral image. Current implementation of the k-means plugin assumes that you have a 2D image with multiple values. To make it work on 3D images you need to iterate over pixels differently, the distance between values though will be measures the same way as for single slice 2D images. Jarek |
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From: Alexandre S. A. <ale...@ph...> - 2013-01-03 16:13:19
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Hello! I am using the k-means segmentation from the ij-plugins toolkit. The segmentation works well for me but i have to extend it to threedimensional data, i.e. a stack of image slices received from X-ray tomography. If i do the segmentation for each picture the problem is that the gray value assigned to a particular phase is not the same for all the pictures. Because of this problem and because of hoping to get even better results i want to implement a real three-dimensional version of the k-means algorithm but i do not know how the "distance" between the pixels is defined. Does anyone know how the "distance" used for the algorithm is defined? Thanks for your help! Alex |
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From: Jarek S. <js...@us...> - 2012-04-11 03:31:53
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ij-plugins Toolkit v.1.6.1 is available at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.6.1/ New: * Plugins > Color > Measure Bands - measures color images and stacks writing results in a single row, rather than a separate row for each band or slice. Works on RGB images or gray level stacks. Improvements: * Stacks created by RGB to CIE L*a*b* and RGB to XYZ converters now have correct labels for each slice (name of the color band). * Updated dependent libraries to recent versions. * Add support for virtual stack to metaimage IO, based on patch provided by Eric Nodwell. * Add help button to plugin options dialog -- Maximum Entropy Multi-Threshold plugin -- k-means Clustering plugin -- Region Growing plugin Developer visible: * Some utility methods added to VectorProcessor and ColorProcessorUtils. * Support for color space conversions with custom white point |
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From: Jarek S. <js...@us...> - 2012-02-23 03:27:36
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A stable version of Scala Console plugin is now available. ij-Scala enables editing and running Scala scripts from ImageJ. Scripts have full access to ImageJ API and API's of all installed ImageJ plugins. The plugin installs under ImageJ menu: Plugins > Scripting > Scala Console Download link: https://sourceforge.net/projects/ij-plugins/files/ij-scala/v.1.0.0/ |
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From: Jarek S. <js...@us...> - 2011-10-16 02:53:13
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ij-dcaw plugin opens raw images from digital cameras in ImageJ with a
help of dcraw tool. The dcraw is a C program created by David Coffin.
Over 200 various raw formats are supported, including Adobe DNG.
New in this release:
* Many new options to control how the raw image is loaded
o Don't automatically brighten the images
o Output color space (raw, sRGB, Adobe, Wide, ProPhoto, XYZ)
o Document mode (no color, no interpolation)
o Document mode without scaling (totally raw)
* Images can be processed in a different directory than original raw
image (if you don't or can't modify its content)
* Added API to simplify calling dcraw wrapper from Java programs.
* Bundled dcraw executable for Windows and Linux updated to the latest
version 9.11 (Date: 2011/10/07 01:00:37)
More info at: http://ij-plugins.sourceforge.net/plugins/dcraw/index.html
Download at:
https://sourceforge.net/projects/ij-plugins/files/ij-dcraw/v.1.3.0/
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From: Jarek S. <js...@us...> - 2011-10-02 15:04:06
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Eric: Thanks for the patch. I will update ij.jar to latest one and incorporate changes. Jarek On 9/30/2011 1:36 PM, Eric Nodwell wrote: > Here's a small patch that adds virtual stack support to ij-plugins, namely: > > - Adds an option to MetaImageReaderPlugin that allows the user to specify whether the MetaImage file should be opened as a virtual stack (just the same as for File -> Import -> Raw). > > - Fixes a small bug that prevented MetaImageWriterPlugin from being able to write images that were virtual stacks. > > One caveat: I used a constructor that only exists in ImageJ 1.44o (which is the currently distributed version of ImageJ), but does NOT exist in ImageJ 1.44i (which is the version distributed with the ij-plugins_toolkit source). Sorry; there didn't seem to be an easy way to support 1.44i and earlier. > > The patch is a unified diff of the src directory. > > Eric > > > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2dcopy2 > > > _______________________________________________ > Ij-plugins-users mailing list > Ij-...@li... > https://lists.sourceforge.net/lists/listinfo/ij-plugins-users |
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From: Eric N. <eri...@nu...> - 2011-09-30 18:03:29
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Here's a small patch that adds virtual stack support to ij-plugins, namely: - Adds an option to MetaImageReaderPlugin that allows the user to specify whether the MetaImage file should be opened as a virtual stack (just the same as for File -> Import -> Raw). - Fixes a small bug that prevented MetaImageWriterPlugin from being able to write images that were virtual stacks. One caveat: I used a constructor that only exists in ImageJ 1.44o (which is the currently distributed version of ImageJ), but does NOT exist in ImageJ 1.44i (which is the version distributed with the ij-plugins_toolkit source). Sorry; there didn't seem to be an easy way to support 1.44i and earlier. The patch is a unified diff of the src directory. Eric |
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From: Jarek S. <js...@us...> - 2009-11-02 19:48:23
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The simplest way to subtract images is like this:
targetImage.copyBits(meanImage, 0, 0, Blitter.SUBTRACT);
Make sure that you images are FloatProcessor, otherwise you will have problems with negative values.
You do not show code that you use for display, so it is hard to say why you have problem there.
Jarek
You wrote:
I have created a mean image out of all the images in a series. Now i would
>like to subtract the mean image from the actual original image. I do it
>something like this
>
> int origSize = targetImage.getWidth() * targetImage.getHeight();
> int subSize = meanImage.getWidth() * meanImage.getHeight();
>
> for (int x = 0; x < meanImage.getWidth(); x++) {
>
> for(int y = 0; y < meanImage.getHeight(); y++) {
> int subPix = meanImage.get(x, y);
> int origPix = targetImage.get(x, y);
> double newPix = origPix - subPix;
>
> targetImage.set(x, y, (int) Math.round(newPix));
> }
> }
>
>
>I don't see the proper effect on the canvas when i apply this? its
>completely blacked out. Any ideas?
|
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From: Jarek S. <js...@us...> - 2009-06-30 02:59:30
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This question is more suitable for the main ImageJ mailing list (http://rsb.info.nih.gov/ij/list.html), as it is not related to ij-plugins. I assume that you refer to http://rsb.info.nih.gov/ij/macros/DrawEllipse.txt macro that draws permanently. Rather than drawing an ellipse you may consider adding and ROI to ROI Manager, then you can show/hide and ROI. Jarek Stephanie Sandhu wrote: > Hello, > I am doing some ImageJ analysis of some cross-sectional areas of mouse > femurs. I am using the DrawEllipses macro to draw the perimeter and > draw major/minor axis but I want to be able to toggle the ellipses > on/off. It would also be nice if I can turn the drawing of the area on > and off as well. Does anyone know how to toggle either of these on/off? > Thanks, > Steph1111 |
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From: Stephanie S. <ste...@ho...> - 2009-06-26 21:07:52
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Hello, I am doing some ImageJ analysis of some cross-sectional areas of mouse femurs. I am using the DrawEllipses macro to draw the perimeter and draw major/minor axis but I want to be able to toggle the ellipses on/off. It would also be nice if I can turn the drawing of the area on and off as well. Does anyone know how to toggle either of these on/off? Thanks, Steph1111 _________________________________________________________________ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290 |
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From: joaomarques <joa...@gm...> - 2009-03-04 14:34:33
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Hi, I'm developing a program that receives a stack of images. Then, it computes the average of all pixels and displays it as a new image. Then, for the program to keep running, I need the user to select a ROI with the mouse. But I don't know how to do that. How do you get the user to select the ROI and after he does the program keeps running? Thanks, João -- View this message in context: http://www.nabble.com/Requesting-the-user-to-select-a-ROI-tp22331229p22331229.html Sent from the ij-plugins-users mailing list archive at Nabble.com. |
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From: Jarek S. <js...@us...> - 2009-01-11 22:17:02
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Kemistry: To see how ImageJ writes JPEG look at method saveAsJpeg(String path) in class ij.io.FileSaver (http://rsb.info.nih.gov/ij/source/ij/io/FileSaver.java), or at method saveAsJpeg(ImagePlus imp, String path) in ij.plugin.JpegWriter class (http://rsb.info.nih.gov/ij/source/ij/plugin/JpegWriter.java). Jarek Kemistry wrote: > I'm new on this forum. > > I would ask you if there's a plugin on the compression jpeg or where i can > take the code that imagej use to save an image in jpeg format. > > Thanks to all and sorry for my english > > Hi |
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From: Jarek S. <js...@us...> - 2008-03-19 01:44:53
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George Mast wrote: > Hello, > > I want to use a plugin in my application. How do I do it? What type of plugins? What types of applications? > > Thanks, > |
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From: George M. <bmw...@ho...> - 2008-03-18 19:28:35
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Hello, I want to use a plugin in my application. How do I do it? Thanks, _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
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From: Jarek S. <js...@us...> - 2008-01-15 04:16:28
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Finally I was able to migrate source code from CVS to SVN. The full commit history is preserved. It was not possible to convert CVS Branches and Tags, though that may not be of much importance. The SVN repository has standard structure with trunk, branches, and tags. Most of the time you want to check out only trunk or one of its subdirectories. As URL of the repository use: https://ij-plugins.svn.sourceforge.net/svnroot/ij-plugins/trunk All members of the ij-plugins project have write access to the repository. The repository can be browsed online at http://ij-plugins.svn.sourceforge.net/viewvc/ij-plugins/trunk/ Jarek |
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From: alineves <ali...@gm...> - 2007-12-06 01:32:18
|
Dear participants After following the known steps for installing vtk plugins in imagej using the compiled binaries from vtk I get the following error message after trying to run the VTK version: VTK native library load failed Caused by; java.lang.UnsatisfiedLinkError: no vtkCommonJava in java.library.path Stack trace: net.sf.ij_plugins.vtk.utils.VTKLoader.loadAll(VTKLoader.java 112) net.sf.ij_plugins.vtk.utils.VTKVersionPlugin.run(VTKVersionPlugin.java:40) ij.IJ.runUserPlugin(IJ.java:158) ij.IJ.runPlugin(IJ.java:124) ij.Executer.runCommand(Executer.java:95) ij.Executer.run(Executer.java:49) java.lang.Thread.run(Thread.java:619) Thanks in advance -- View this message in context: http://www.nabble.com/Problem-installing-vtk-filters-tf4953505.html#a14184705 Sent from the ij-plugins-users mailing list archive at Nabble.com. |