Hi folks,
Does anyone know how to prevent an ImageJ ImageWindow from closing? I currently have images being displayed to an ImageWindow, and everything works well, until someone inadvertently closes the window. I know how to deal with this in Swing, but not AWT... Thanks! Jeff ---------------------------------------------- Jeff Hardin Professor and Chair, Department of Zoology Director, Biology Core Curriculum University of Wisconsin 1117 W. Johnson St. Madison, WI 53706 voice: (608) 262-9634 fax: (608) 262-7319 email: [hidden email] On Jul 9, 2008, at 11:00 PM, IMAGEJ automatic digest system wrote: > There are 11 messages totalling 644 lines in this issue. > > Topics of the day: > > 1. Grains analysis in metals > 2. Two color detection + segmentation > 3. how to measure (4) > 4. question with regard to image analysis (2) > 5. [ImageJ macro] roiManager+setBatchMode leads to "out of memory" > (sometimes) > 6. New: MovieIO - A Simple Video Processing Library for ImageJ > 7. 3D filtering > > ---------------------------------------------------------------------- > > Date: Wed, 9 Jul 2008 05:42:47 -0400 > From: Sami Badawi <[hidden email]> > Subject: Re: Grains analysis in metals > > Hi Laurent, > > The ShapeLogic plugin contains a particle analyzer that works directly > on gray scale and color images. This might work for you but it only > works if you have grains in a relatively uniform background, not if > you only have grains and boundaries. > > It collects these particle properties: > * Area > * Center of gravity > * Color > * Std dev for color > * Length of perimeter > * Circularity > * Gray value brightness > * Bounding box > * Number of hard corners > * Number of inflection points > * Number of curve arches > > Link: http://www.shapelogic.org/particle.html > > -Sami Badawi > http://www.shapelogic.org > > ------------------------------ > > Date: Wed, 9 Jul 2008 14:18:51 +0200 > From: "Usaj, Marko" <[hidden email]> > Subject: Two color detection + segmentation > > Hello everybody! > > I have following problem: > > I have fluorescence images 1 with objects (intensity) 1 and > fluorescence = > images 2 with objects (intensity) 2. But some of object are the same = > (fused) I want to find how many (percent) object are dual color. > > Ok, one option is segmentation and then comparison/color align and > then = > counting. > > But i hear that similar procedure is to just compare pixel > intensity, = > and perform percent calculation using number of pixels instead of > object = > (dual color/all). Is there any plug in for do that? > > Second questions is about uneven illumination. Can anyone suggest > good = > plugin who deal with that.=20 > > Third questions is fluorescence thresholding/segment fluorescence > nuclei = > of cells. Which is good algorithm/plugin for that?=20 > > Regardss=20 > > Marko > =20 > > ------------------------------ > > Date: Wed, 9 Jul 2008 21:28:24 +0200 > From: Johannes Breu <[hidden email]> > Subject: how to measure > > Hello, > > because I am quite unexperienced in measuring fluorescent signals I > hope > somebody may give me some fruitful instructions for doing with imageJ. > > Transfected HEK cells (expressing a presynaptic protein -green > channel) wer= > e > cocultured with hippocampal cells. I wish to measure the signals of a > postsynaptic proteins (red channel) on transfected HEK cells. In other > words: I am interested to measure the overlap between the red an the > green > channel. > > My idea was to mark the green signal (transfected HEK cells) and to > measure > the intensities in the red channel. > > I did it that way: > 1) Fusing stacks (Image-Hyperstack-Reduce Dimensionality) > 2) Make it possible to switch between channels (Image-Hyperstack- > Channels) > 3) Mark the green signal with the freehand tool and then switch to > the red > channel. > 4) Measure the intensities of the red signal within the marked area > (Analyze-Measure). > > I feel there is a better more efficient way to do. Is there? > Especially the > method to define the region of interest (the overlap) could be more > precise= > , > couldn=B4t it... > > Thanks Johannes > > ------------------------------ > > Date: Wed, 9 Jul 2008 15:25:21 -0400 > From: Junghyo Jo <[hidden email]> > Subject: question with regard to image analysis > > Dear Image J experts, > I am wondering if ImageJ can analyze the following work? > I want to count double staining cells within a tissue boundary. > > Although I am not familiar with ImageJ, > I imagine that to conduct this work, > ImageJ has to set the specific tissue boundary > on the sample image. > Then, it has to separately count two kinds of staining cells > which lies within the given tissue boundary. > Finally, it has to determine the double staining cells > based on the above information. > In the sample image, all nuclei of cells are stained with blue. > Is this procedure possible in ImageJ? > > I appreciate your comment about this question. > > Sincerely, > Junghyo > > ------------------------------ > > Date: Wed, 9 Jul 2008 15:29:47 -0400 > From: Wayne Rasband <[hidden email]> > Subject: Re: [ImageJ macro] roiManager+setBatchMode leads to "out > of memory" (sometimes) > >> Hello ImageJers, >> >> When I run the following macro (in order to "rotate" a bunch of ROIs >> in the ROIManager), I get an "out of memory" error after a hundred of >> rois has been processed . >> If I comment out the setBatchMode lines, it works (but much slower). >> It might be related to the roiManager, I wrote another macro >> duplicating and rotating images in batchmode, without any issue. >> I tested on OS 10.5 and winXP (jvm1.6_03) with ij1.41g/h with the >> same results, not yet tested on linux >> using "Monitor Memory", one can see the macro eating memory quite >> fast. >> I uploaded a sample "source" image and a quite big ROI set there: >> >> http://xfer.curie.fr/get/gYrE1HY3BYl/OutOfMemSamples.tar >> >> I tried to summon ij.IJ.freeMemory and friends as seen in a former >> thread on the list, but it didn't help. >> It seems to be a bit more difficult than I expected. >> Any hint? >> Thanks > > This bug is fixed in the v1.41h daily build. The ROI Manager "Update" > option was saving a reference to the image, which prevented it from > being garbage collected. There is also a small bug in the macro that > causes it to fail if the background color is not black. This can be > fixed by adding > > setBackgroundColor(0, 0, 0); > > -wayne > > >> sebastien >> >> (off topic: I couldn't simply copy and fill all rois on a new black >> image, rotate and use "analyze particles" to populate the roi >> manager cause close rois/particles were joined after rotation.) >> >> >> macro "rotateROIs [F1]" >> { >> srcpath = File.openDialog("Source image?"); >> roispath = File.openDialog("Roi set?"); >> open(srcpath); >> sid = getImageID(); >> roiManager("reset"); >> open(roispath); >> rot_angle = getNumber("Rot Angle", 5); >> setBatchMode(true); >> rois_rotateAll(sid, rot_angle); >> setBatchMode(false); >> } >> >> >> function rois_rotateAll(srcid, angle) >> { >> iter = 0; >> roicnt = roiManager("count"); >> oldroicnt = roicnt; >> run("Set Measurements...", "area mean min integrated limit >> redirect=None decimal=3"); >> setForegroundColor(255, 255, 255); >> i = 0 ; >> while ( i < roicnt ) >> { >> selectImage(srcid); >> run("Select All"); >> run("Duplicate...", "title=TMP_ROIS_masks"); >> dupid = getImageID(); >> run("Select All"); >> run("Cut"); >> run("8-bit"); >> setVoxelSize(1, 1, 1, "pixels"); >> roiManager("Select", i); >> roiManager("Fill"); >> run("Select None"); >> run("Arbitrarily...", "angle=" + angle + " grid=1 interpolate >> enlarge"); >> setThreshold(250,255); >> run("Select None"); >> run("Clear Results"); >> run("Analyze Particles...", "size=5-Infinity >> circularity=0.00-1.00 show=Nothing exclude clear include record"); >> if ( nResults == 1 ) >> { >> x = getResult("XStart", 0); >> y = getResult("YStart", 0); >> doWand(x, y); >> roiManager("Update"); >> i++; >> } >> else >> { >> print("warning: rotation of roi " + i + " gives unexpected >> number of results: " + nResults); >> print("warning: deletion of roi "+ i); >> roiManager("Delete"); >> roicnt--; >> } >> selectImage(dupid); >> run("Select None"); >> close(); >> //useless call to freeMemory every 10 iterations >> //iter++; >> //if ( (iter % 10) ==0) >> // { >> // print(call("ij.IJ.freeMemory")); >> // wait(1000); >> //} >> } >> } >> > > ------------------------------ > > Date: Wed, 9 Jul 2008 22:14:24 +0200 > From: Burger Wilhelm <[hidden email]> > Subject: New: MovieIO - A Simple Video Processing Library for ImageJ > > Hello ImageJ folks, > =20 > I would like to share a small library for ImageJ for reading and > writing = > video files. Why another video package? - I needed something *very* = > simple to pass on to my students. > =20 > This library reads and writes video files frame-by-frame under the = > control of a simple loop, using only a *single* ImageProcessor > object. = > No callbacks or events are used, the library does not rely on stacks > and = > thus has only modest memory requirements. Thus videos of arbitrary = > length (even HD formats) can be processed.=20 > =20 > The library is implemented transparently in 2 versions - JMF and = > QuickTime -, which can be used alternatively or together. If only > one = > version is used, the other package can be easily removed. Here is a = > typical code sequence using the QuickTime version to illustrate how > a = > video file is read and processed frame by frame: > =20 > String path =3D "AppleQtSample.mov"; > MovieReader mr =3D QtMovieReader.openMovie(path); > ImageProcessor ip =3D mr.createImageProcessor(); > int frame; > while ((frame =3D mr.getNextFrame(ip)) >=3D 0) { > //process and/or display the frame contained in ip ... > } > mr.close(); > =20 > Note that this is no production code but aims at Java plugin > developers. = > Several example plugins are provided.=20 > Currently the package is only tested under Windows XP (32 bits) - = > reports for other platforms and suggestions are welcome! > =20 > Download from: http://staff.fh-hagenberg.at/burger/imagej/ > =20 > Hope this is useful- > Wilhelm > www.imagingbook.com > =20 > =20 > > ------------------------------ > > Date: Wed, 9 Jul 2008 15:42:21 -0400 > From: Joel Sheffield <[hidden email]> > Subject: Re: question with regard to image analysis > > Hi Junghyo, > > In principle, the answer is yes. As a practical matter, it will > depend very much on your images. It would be very helpful if you > could post an example of your data for the list to see. > > Joel > > >> Dear Image J experts, >> I am wondering if ImageJ can analyze the following work? >> I want to count double staining cells within a tissue boundary. >> >> Although I am not familiar with ImageJ, >> I imagine that to conduct this work, >> ImageJ has to set the specific tissue boundary >> on the sample image. >> Then, it has to separately count two kinds of staining cells >> which lies within the given tissue boundary. >> Finally, it has to determine the double staining cells >> based on the above information. >> In the sample image, all nuclei of cells are stained with blue. >> Is this procedure possible in ImageJ? >> >> I appreciate your comment about this question. >> >> Sincerely, >> Junghyo > > > -- > Joel B. Sheffield, Ph.D. > Biology Department, Temple University > 1900 North 12th Street > Philadelphia, PA 19122 > [hidden email] > (215) 204 8839, fax (215) 204 0486 > http://astro.temple.edu/~jbs > > ------------------------------ > > Date: Wed, 9 Jul 2008 16:15:49 -0400 > From: Joel Sheffield <[hidden email]> > Subject: Re: how to measure > > It looks to me as if you should look at some of the colocalization > plugins. These allow you to select just those cells that share both > labels, as long as the labels are in the same part of the cell. > > > >> Hello, >> >> because I am quite unexperienced in measuring fluorescent signals I >> hope >> somebody may give me some fruitful instructions for doing with >> imageJ. >> >> Transfected HEK cells (expressing a presynaptic protein -green >> channel) = > were >> cocultured with hippocampal cells. I wish to measure the signals of a >> postsynaptic proteins (red channel) on transfected HEK cells. In >> other >> words: I am interested to measure the overlap between the red an >> the gre= > en >> channel. >> >> My idea was to mark the green signal (transfected HEK cells) and to >> meas= > ure >> the intensities in the red channel. >> >> I did it that way: >> 1) Fusing stacks (Image-Hyperstack-Reduce Dimensionality) >> 2) Make it possible to switch between channels (Image-Hyperstack- >> Channel= > s) >> 3) Mark the green signal with the freehand tool and then switch to >> the r= > ed >> channel. >> 4) Measure the intensities of the red signal within the marked area >> (Analyze-Measure). >> >> I feel there is a better more efficient way to do. Is there? >> Especially = > the >> method to define the region of interest (the overlap) could be more >> prec= > ise, >> couldn=B4t it... >> >> Thanks Johannes > > > -- > Joel B. Sheffield, Ph.D. > Biology Department, Temple University > 1900 North 12th Street > Philadelphia, PA 19122 > [hidden email] > (215) 204 8839, fax (215) 204 0486 > http://astro.temple.edu/~jbs > > ------------------------------ > > Date: Wed, 9 Jul 2008 17:51:40 -0300 > From: "Ruy G. Jaeger" <[hidden email]> > Subject: Re: how to measure > > Johannes > > I also believe you need to do colocalization analysis. Try JACoP > =20 > (Just Another Co-localization Plugin) plug from Fabrice P. =20 > Cordeli=E8res. Here goes the site: > > http://rsbweb.nih.gov/ij/plugins/track/jacop.html > > Ruy Jaeger > > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D > Ruy G. Jaeger, DDS, MSD, PhD > University of Sao Paulo - USP Institute of Biomedical Sciences > - ICB > Department of Cell and Developmental Biology > Av. Prof. Lineu Prestes 1524 > Ed Biomedicas 1 rooms 302 (office and microscopy room) and > 405(Laborator= > y) > Sao Paulo SP 05508 000 BRAZIL > Phones:55-11-30918454(office), 55-1130918034 (Lab);Fax: > 55-11-30917402 > email:[hidden email] website: http://www.icb.usp.br/~rgjaeger/index.h= > tml > =20 > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D > > > > Citando Joel Sheffield <[hidden email]>: > >> It looks to me as if you should look at some of the colocalization >> plugins. These allow you to select just those cells that share both >> labels, as long as the labels are in the same part of the cell. >> >> >> >>> Hello, >>> >>> because I am quite unexperienced in measuring fluorescent signals >>> I hope >>> somebody may give me some fruitful instructions for doing with >>> imageJ. >>> >>> Transfected HEK cells (expressing a presynaptic protein -green >>> channel) w= > ere >>> cocultured with hippocampal cells. I wish to measure the signals >>> of a >>> postsynaptic proteins (red channel) on transfected HEK cells. In >>> other >>> words: I am interested to measure the overlap between the red an >>> the gree= > n >>> channel. >>> >>> My idea was to mark the green signal (transfected HEK cells) and >>> to measu= > re >>> the intensities in the red channel. >>> >>> I did it that way: >>> 1) Fusing stacks (Image-Hyperstack-Reduce Dimensionality) >>> 2) Make it possible to switch between channels (Image-Hyperstack- >>> Channels= > ) >>> 3) Mark the green signal with the freehand tool and then switch to >>> the re= > d >>> channel. >>> 4) Measure the intensities of the red signal within the marked area >>> (Analyze-Measure). >>> >>> I feel there is a better more efficient way to do. Is there? >>> Especially t= > he >>> method to define the region of interest (the overlap) could be >>> more preci= > se, >>> couldn=B4t it... >>> >>> Thanks Johannes >> >> >> -- >> Joel B. Sheffield, Ph.D. >> Biology Department, Temple University >> 1900 North 12th Street >> Philadelphia, PA 19122 >> [hidden email] >> (215) 204 8839, fax (215) 204 0486 >> http://astro.temple.edu/~jbs >> > > ------------------------------ > > Date: Wed, 9 Jul 2008 23:31:55 +0200 > From: Johannes Breu <[hidden email]> > Subject: Re: how to measure > > I tried some of the recommended plugins (under those JACoP seems to > be the > most intuitive) but I never found the right subtool... I am not > interested > in measuring the degree of colocalization. I just want to measure > fluorescent intensities of the red channel while I defined the ROI > in the > green channel. Are the colocalization plugins really the right tools? > > 2008/7/9 Ruy G. Jaeger <[hidden email]>: > >> Johannes >> >> I also believe you need to do colocalization analysis. Try JACoP >> (Just >> Another Co-localization Plugin) plug from Fabrice P. >> Cordeli=E8res. Here= > goes >> the site: >> >> http://rsbweb.nih.gov/ij/plugins/track/jacop.html >> >> Ruy Jaeger >> >> >> = >> 3D >> = >> 3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D >> Ruy G. Jaeger, DDS, MSD, PhD >> University of Sao Paulo - USP Institute of Biomedical Sciences >> - ICB >> Department of Cell and Developmental Biology >> Av. Prof. Lineu Prestes 1524 >> Ed Biomedicas 1 rooms 302 (office and microscopy room) and >> 405(Laboratory) >> Sao Paulo SP 05508 000 BRAZIL >> Phones:55-11-30918454(office), 55-1130918034 (Lab);Fax: >> 55-11-30917402 >> email:[hidden email] <email%[hidden email]> website: >> http://www.icb.usp.br/~rgjaeger/index.html<http://www.icb.usp.br/%7Ergjae= > ger/index.html> >> >> = >> 3D >> = >> 3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > = > 3D > = > 3D > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D >> >> >> >> Citando Joel Sheffield <[hidden email]>: >> >> >> It looks to me as if you should look at some of the colocalization >>> plugins. These allow you to select just those cells that share both >>> labels, as long as the labels are in the same part of the cell. >>> >>> >>> >>> Hello, >>>> >>>> because I am quite unexperienced in measuring fluorescent signals >>>> I hop= > e >>>> somebody may give me some fruitful instructions for doing with >>>> imageJ. >>>> >>>> Transfected HEK cells (expressing a presynaptic protein -green >>>> channel) >>>> were >>>> cocultured with hippocampal cells. I wish to measure the signals >>>> of a >>>> postsynaptic proteins (red channel) on transfected HEK cells. In >>>> other >>>> words: I am interested to measure the overlap between the red an >>>> the >>>> green >>>> channel. >>>> >>>> My idea was to mark the green signal (transfected HEK cells) and to >>>> measure >>>> the intensities in the red channel. >>>> >>>> I did it that way: >>>> 1) Fusing stacks (Image-Hyperstack-Reduce Dimensionality) >>>> 2) Make it possible to switch between channels >>>> (Image-Hyperstack-Channels) >>>> 3) Mark the green signal with the freehand tool and then switch >>>> to the >>>> red >>>> channel. >>>> 4) Measure the intensities of the red signal within the marked area >>>> (Analyze-Measure). >>>> >>>> I feel there is a better more efficient way to do. Is there? >>>> Especially >>>> the >>>> method to define the region of interest (the overlap) could be more >>>> precise, >>>> couldn=B4t it... >>>> >>>> Thanks Johannes >>>> >>> >>> >>> -- >>> Joel B. Sheffield, Ph.D. >>> Biology Department, Temple University >>> 1900 North 12th Street >>> Philadelphia, PA 19122 >>> [hidden email] >>> (215) 204 8839, fax (215) 204 0486 >>> http://astro.temple.edu/~jbs <http://astro.temple.edu/%7Ejbs> >>> >>> > > ------------------------------ > > Date: Wed, 9 Jul 2008 23:31:55 -0400 > From: Robert Edward Martin <[hidden email]> > Subject: 3D filtering > > Hi All, > > > I am looking to implement a 3D convolution for filtering at different > wavelengths of stack data. THis would be a relatively easy extension > of the 2D filtering yet I can not find a package that does this. > > Does anyone know where I can download a copy of a 3D filtering process > with adjustable filter coefficients (or even without)? > > Thanks so much > > Robert > > ------------------------------ > > End of IMAGEJ Digest - 8 Jul 2008 to 9 Jul 2008 (#2008-184) > *********************************************************** |
Hi,
On Thu, 10 Jul 2008, Jeff Hardin wrote: > Does anyone know how to prevent an ImageJ ImageWindow from closing? I > currently have images being displayed to an ImageWindow, and everything > works well, until someone inadvertently closes the window. I know how to > deal with this in Swing, but not AWT... AFAICT you could extend ImageWindow, overloading windowClosing() so that it does not dispose(). Then set this newly created ImageWindow. A much dirtier solution is to extend ImageWindow with a static method setting your _real_ ImageWindow's 'closed' property to true. Hth, Dscho P.S.: BTW you _did_ have to quote the whole unrelated digested mail, wasting everybody's bandwidth, didn't you? |
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