http://imagej.273.s1.nabble.com/Preventing-an-ImageWindow-from-closing-tp3695624.html
everything works well, until someone inadvertently closes the window.
1117 W. Johnson St.
> 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)
> ***********************************************************