ImageJ Reslice command (Image-Stacks->Reslice)

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ImageJ Reslice command (Image-Stacks->Reslice)

Ronny Shalev
I was wondering if anyone knows where I can find the Reslice algorithm
description/explanation.

I am learning image processing and analysis on my own and I find ImageJ
extrimly helpful. Now, I am trying to understand the inner workings of some
of the functions.

I greatly appreciate the help.

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Re: ImageJ Reslice command (Image-Stacks->Reslice)

Philippe CARL
Dear Ronny,
Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press "l") and then type the tool name you are looking for.
In your case, just type "resl" will already be enough to locate the "reslice" tool.
From there you will see that the tool path within ImageJ is "Image>Stacks" and that it's code with within the class "ij.plugin.Slicer".
Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) then go to "Developer Resources->Browsable Source" (https://imagej.nih.gov/ij/developer/source/index.html) and locate "ij.plugin.Slicer".to find the "Slicer.java" file and there you can enjoy the source code you are looking for!!!
My best regards,
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Ronny Shalev
Envoyé : jeudi 28 septembre 2017 00:22
À : [hidden email]
Objet : ImageJ Reslice command (Image-Stacks->Reslice)

I was wondering if anyone knows where I can find the Reslice algorithm description/explanation.

I am learning image processing and analysis on my own and I find ImageJ extrimly helpful. Now, I am trying to understand the inner workings of some of the functions.

I greatly appreciate the help.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: ImageJ Reslice command (Image-Stacks->Reslice)

ctrueden
Hi Phillipe and everyone,

In the Command Finder, you can also click the "Source" button to jump
directly to the source code on the ImageJ 1.x web site.

The source can also be browsed on GitHub:
    https://github.com/imagej/imagej1

Press the T key to search for specific files.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Sep 28, 2017 at 2:36 AM, Philippe CARL <[hidden email]>
wrote:

> Dear Ronny,
> Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press
> "l") and then type the tool name you are looking for.
> In your case, just type "resl" will already be enough to locate the
> "reslice" tool.
> From there you will see that the tool path within ImageJ is "Image>Stacks"
> and that it's code with within the class "ij.plugin.Slicer".
> Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) then
> go to "Developer Resources->Browsable Source" (https://imagej.nih.gov/ij/
> developer/source/index.html) and locate "ij.plugin.Slicer".to find the
> "Slicer.java" file and there you can enjoy the source code you are looking
> for!!!
> My best regards,
> Philippe
>
> Philippe CARL
> Laboratoire de Biophotonique et Pharmacologie
> UMR 7213 CNRS - Université de Strasbourg
> Faculté de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : +33(0)3 68 85 41 84
>
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Ronny Shalev
> Envoyé : jeudi 28 septembre 2017 00:22
> À : [hidden email]
> Objet : ImageJ Reslice command (Image-Stacks->Reslice)
>
> I was wondering if anyone knows where I can find the Reslice algorithm
> description/explanation.
>
> I am learning image processing and analysis on my own and I find ImageJ
> extrimly helpful. Now, I am trying to understand the inner workings of some
> of the functions.
>
> I greatly appreciate the help.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: ImageJ Reslice command (Image-Stacks->Reslice)

Ronny Shalev
Thanks for the input, Philippe and Curtis,

I was wondering if there exists a paper discussing the algorithm as a
concept (and, maybe pseudo code). If I need to understand the algorithm via
reading the code, I will need to learn Java, which might take sometime as I
am working on Python right now.

Regards

Ronny

On Thu, Sep 28, 2017 at 5:37 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Phillipe and everyone,
>
> In the Command Finder, you can also click the "Source" button to jump
> directly to the source code on the ImageJ 1.x web site.
>
> The source can also be browsed on GitHub:
>     https://github.com/imagej/imagej1
>
> Press the T key to search for specific files.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, Sep 28, 2017 at 2:36 AM, Philippe CARL <[hidden email]>
> wrote:
>
> > Dear Ronny,
> > Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press
> > "l") and then type the tool name you are looking for.
> > In your case, just type "resl" will already be enough to locate the
> > "reslice" tool.
> > From there you will see that the tool path within ImageJ is
> "Image>Stacks"
> > and that it's code with within the class "ij.plugin.Slicer".
> > Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) then
> > go to "Developer Resources->Browsable Source" (
> https://imagej.nih.gov/ij/
> > developer/source/index.html) and locate "ij.plugin.Slicer".to find the
> > "Slicer.java" file and there you can enjoy the source code you are
> looking
> > for!!!
> > My best regards,
> > Philippe
> >
> > Philippe CARL
> > Laboratoire de Biophotonique et Pharmacologie
> > UMR 7213 CNRS - Université de Strasbourg
> > Faculté de Pharmacie
> > 74 route du Rhin
> > 67401 ILLKIRCH
> > Tel : +33(0)3 68 85 41 84
> >
> > -----Message d'origine-----
> > De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> > Ronny Shalev
> > Envoyé : jeudi 28 septembre 2017 00:22
> > À : [hidden email]
> > Objet : ImageJ Reslice command (Image-Stacks->Reslice)
> >
> > I was wondering if anyone knows where I can find the Reslice algorithm
> > description/explanation.
> >
> > I am learning image processing and analysis on my own and I find ImageJ
> > extrimly helpful. Now, I am trying to understand the inner workings of
> some
> > of the functions.
> >
> > I greatly appreciate the help.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ronny Shalev, PhD

Cell: 216-543-6596

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Re: ImageJ Reslice command (Image-Stacks->Reslice)

ctrueden
Hi Ronny,

> I was wondering if there exists a paper discussing the algorithm as a
> concept

There is user documentation in the ImageJ user manual:
https://imagej.net/docs/guide/146-28.html#sub:Reslice...[/]

No paper though.

> If I need to understand the algorithm via reading the code, I will
> need to learn Java, which might take sometime as I am working on
> Python right now.

Fortunately, Java syntax is quite similar to Python. Reading the source
code will be your best bet to understand the algorithm here.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Sep 28, 2017 at 4:54 PM, Ronny Shalev <[hidden email]> wrote:

> Thanks for the input, Philippe and Curtis,
>
> I was wondering if there exists a paper discussing the algorithm as a
> concept (and, maybe pseudo code). If I need to understand the algorithm via
> reading the code, I will need to learn Java, which might take sometime as I
> am working on Python right now.
>
> Regards
>
> Ronny
>
> On Thu, Sep 28, 2017 at 5:37 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Phillipe and everyone,
> >
> > In the Command Finder, you can also click the "Source" button to jump
> > directly to the source code on the ImageJ 1.x web site.
> >
> > The source can also be browsed on GitHub:
> >     https://github.com/imagej/imagej1
> >
> > Press the T key to search for specific files.
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Thu, Sep 28, 2017 at 2:36 AM, Philippe CARL <[hidden email]
> >
> > wrote:
> >
> > > Dear Ronny,
> > > Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press
> > > "l") and then type the tool name you are looking for.
> > > In your case, just type "resl" will already be enough to locate the
> > > "reslice" tool.
> > > From there you will see that the tool path within ImageJ is
> > "Image>Stacks"
> > > and that it's code with within the class "ij.plugin.Slicer".
> > > Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/)
> then
> > > go to "Developer Resources->Browsable Source" (
> > https://imagej.nih.gov/ij/
> > > developer/source/index.html) and locate "ij.plugin.Slicer".to find the
> > > "Slicer.java" file and there you can enjoy the source code you are
> > looking
> > > for!!!
> > > My best regards,
> > > Philippe
> > >
> > > Philippe CARL
> > > Laboratoire de Biophotonique et Pharmacologie
> > > UMR 7213 CNRS - Université de Strasbourg
> > > Faculté de Pharmacie
> > > 74 route du Rhin
> > > 67401 ILLKIRCH
> > > Tel : +33(0)3 68 85 41 84
> > >
> > > -----Message d'origine-----
> > > De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> > > Ronny Shalev
> > > Envoyé : jeudi 28 septembre 2017 00:22
> > > À : [hidden email]
> > > Objet : ImageJ Reslice command (Image-Stacks->Reslice)
> > >
> > > I was wondering if anyone knows where I can find the Reslice algorithm
> > > description/explanation.
> > >
> > > I am learning image processing and analysis on my own and I find ImageJ
> > > extrimly helpful. Now, I am trying to understand the inner workings of
> > some
> > > of the functions.
> > >
> > > I greatly appreciate the help.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ronny Shalev, PhD
>
> Cell: 216-543-6596
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Set Measurement failed in macro

Straatman, Kees (Dr.)
Dear list


I noticed some strange behaviour when using different Set Measurements together with the ROI manager in a macro.


example code


run("Blobs (25K)");
setAutoThreshold("Default");
setOption("BlackBackground", false);
run("Convert to Mask");
run("Set Measurements...", "display redirect=None decimal=0");
run("Analyze Particles...", "size=1-Infinity summarize add");
run("Set Measurements...", "feret's display redirect=None decimal=3");
roiManager("Measure");

As soon as the second Set Measurements runs area data is already displayed in the Results window, even before anything is measured, labelled as blobs.gif. The last line adds a second series of data to the Results table now labelled as ROIs but still the results are for area and not feret's data. Strangely enough the first few times the values for area were the correct values but after I moved some code around they now show zeros.

Also hitting "Measure" in the ROI menu after running the macro still gives the same result. Checking the settings under Analyze > Set Measurements shows however that Feret's diameter is selected and not Area.

I have tested it on several PCs, all Windows 7 using the latest updated version of Fiji.

So it seems to be that there is somewhere a bug.

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility>


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Re: Set Measurement failed in macro

Herbie
Good day Kees,

after running your macro I think I see what you mean...

My impression is, that "Set Measurements..." was intended to be used
only once (at the beginning) of a macro but I may be wrong and others
may confirm that the described behavior appears at least as strange.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::
Am 05.10.17 um 21:50 schrieb Straatman, Kees (Dr.):

> Dear list
>
>
> I noticed some strange behaviour when using different Set
> Measurements together with the ROI manager in a macro.
>
>
> example code
>
>
> run("Blobs (25K)"); setAutoThreshold("Default");
> setOption("BlackBackground", false); run("Convert to Mask"); run("Set
> Measurements...", "display redirect=None decimal=0"); run("Analyze
> Particles...", "size=1-Infinity summarize add"); run("Set
> Measurements...", "feret's display redirect=None decimal=3");
> roiManager("Measure");
>
> As soon as the second Set Measurements runs area data is already
> displayed in the Results window, even before anything is measured,
> labelled as blobs.gif. The last line adds a second series of data to
> the Results table now labelled as ROIs but still the results are for
> area and not feret's data. Strangely enough the first few times the
> values for area were the correct values but after I moved some code
> around they now show zeros.
>
> Also hitting "Measure" in the ROI menu after running the macro still
> gives the same result. Checking the settings under Analyze > Set
> Measurements shows however that Feret's diameter is selected and not
> Area.
>
> I have tested it on several PCs, all Windows 7 using the latest
> updated version of Fiji.
>
> So it seems to be that there is somewhere a bug.
>
> Best wishes
>
> Kees
>
> Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging
> Facility Centre for Core Biotechnology Services University of
> Leicester
> www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility>
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
®

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Re: Set Measurement failed in macro

Wayne Rasband-2
In reply to this post by Straatman, Kees (Dr.)
> On Oct 5, 2017, at 3:50 PM, Straatman, Kees (Dr.) <[hidden email]> wrote:
>
> Dear list
>
> I noticed some strange behaviour when using different Set Measurements together with the ROI manager in a macro.
>
> example code
>
> run("Blobs (25K)");
> setAutoThreshold("Default");
> setOption("BlackBackground", false);
> run("Convert to Mask");
> run("Set Measurements...", "display redirect=None decimal=0");
> run("Analyze Particles...", "size=1-Infinity summarize add");
> run("Set Measurements...", "feret's display redirect=None decimal=3");
> roiManager("Measure");
>
> As soon as the second Set Measurements runs area data is already displayed in the Results window, even before anything is measured, labelled as blobs.gif. The last line adds a second series of data to the Results table now labelled as ROIs but still the results are for area and not feret's data. Strangely enough the first few times the values for area were the correct values but after I moved some code around they now show zeros.
>
> Also hitting "Measure" in the ROI menu after running the macro still gives the same result. Checking the settings under Analyze > Set Measurements shows however that Feret's diameter is selected and not Area.
>
> I have tested it on several PCs, all Windows 7 using the latest updated version of Fiji.
>
> So it seems to be that there is somewhere a bug.


Dear Kees,

This bug is fixed in the latest ImageJ daily build (1.51r18). Or work around it by adding

    run("Clear Results”);

after running the particle analyzer, as in this version of your test macro:

  run("Blobs (25K)");
  setAutoThreshold("Default");
  setOption("BlackBackground", false);
  run("Convert to Mask");
  run("Set Measurements...", "display redirect=None decimal=0");
  run("Analyze Particles...", "size=1-Infinity summarize add");
  run("Clear Results");
  run("Set Measurements...", "feret's display redirect=None decimal=3");
  roiManager("Measure”);

-wayne

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