heat map

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heat map

Szilvi Mezey
Dear All,

I've been tangled up in a problem with ImageJ and hope to find somebody who
can help...

I'm trying to turn a thresholded image into a heat map, where different
colours indicate the density of black pixels in a given area. More labelling
would be red, changing to green and then blue in areas with less labelling
and white is no label at all. Is there any way of doing this in ImageJ?
Can't find any macros or plugins (not even any kind of free software), even
though I'm sure I'm not the first to tackle this problem.

Hope somebody can help...

Szilvia Mezey
Semmelweis University
Budapest, Hungary
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Re: heat map

Gabriel Landini
On Thursday 26 November 2009  13:46:07 Szilvia Mezey wrote:
> I've been tangled up in a problem with ImageJ and hope to find somebody who
> can help...
>
> I'm trying to turn a thresholded image into a heat map, where different
> colours indicate the density of black pixels in a given area. More labelling
> would be red, changing to green and then blue in areas with less labelling
> and white is no label at all. Is there any way of doing this in ImageJ?
> Can't find any macros or plugins (not even any kind of free software), even
> though I'm sure I'm not the first to tackle this problem.

Run a mean filter of size of your local region.
Apply some LUT such as "fire"
The colour will vary depending on the mean value of the set pixels in a region
given by the filter kernel size centred at that location.

Cheers

G.
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Re: heat map

Szilvi Mezey
Gabriel,

thank you very much, it works a treat! I've also found an LUT called
"thermal" which does the job perfectly.

Szilvi

2009/11/26 Gabriel Landini <[hidden email]>

> On Thursday 26 November 2009  13:46:07 Szilvia Mezey wrote:
> > I've been tangled up in a problem with ImageJ and hope to find somebody
> who
> > can help...
> >
> > I'm trying to turn a thresholded image into a heat map, where different
> > colours indicate the density of black pixels in a given area. More
> labelling
> > would be red, changing to green and then blue in areas with less
> labelling
> > and white is no label at all. Is there any way of doing this in ImageJ?
> > Can't find any macros or plugins (not even any kind of free software),
> even
> > though I'm sure I'm not the first to tackle this problem.
>
> Run a mean filter of size of your local region.
> Apply some LUT such as "fire"
> The colour will vary depending on the mean value of the set pixels in a
> region
> given by the filter kernel size centred at that location.
>
> Cheers
>
> G.
>
>
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What's wrong here?

Herbert M. Geller
In reply to this post by Szilvi Mezey
 From other macros, I cobbled together a macro that will batch convert
all files to 8-bit grey scale from 24 bit color and saves them with a
different name.  (The built-in batch convert function does not 1) go to
grey scale and 2) does not change the file name). Yes it returns an
error about the file type in the target directory being wrong.  I get
the same error when I run the Batch convert macro.
Has something changed that causes this problem?
Thanks!

// These macros convert all the files in a folder to a different format.
// Two dialog boxes are displayed. Select the source folder in the
// first and the destination folder in the second.

  macro "Batch Convert to 8-bit TIFF" {convert("8-bit tiff");}


  function convert(format) {
      requires("1.33s");
      dir1 = getDirectory("Choose Source Directory ");
      dir2 = getDirectory("Choose Destination Directory ");
      list = getFileList(dir1);
      setBatchMode(true);
      for (i=0; i<list.length; i++) {
          showProgress(i+1, list.length);
        path = dir1+list[i];
          open(path);
          if (startsWith(format, "8-bit")) convertTo8Bit();
     run("8-bit");
    dotIndex = lastIndexOf(path, ".");
          if (dotIndex!=-1)
              path = substring(path, 0, dotIndex); // remove extension
          save(path+"-8bit.tif");
          close();
      }
  }

  function convertTo8Bit() {
      if (bitDepth==24)
          run("8-bit Color", "number=256");
      else
          run("8-bit");
  }

--
--------------------------------------
Herbert M. Geller, Ph.D.
Developmental Neurobiology Section
National Heart Lung and Blood Institute, NIH
10 Center Drive MSC 1754
Bldg 10, Room 6D18
Bethesda, MD  20892-1754
Tel: 301-451-9440; Fax: 301-594-8133
e-mail: [hidden email]
Web: http://dir.nhlbi.nih.gov/labs/ldn/index.asp
---------------------------------------