Looking for tissue segmentation plugin

[ard]

In Fiji we have the Color Inspector 3D, the Cell Counter plugin, Color Deconvolution and the Color Segmentation option.
I'm looking for a combo of these; to interactively decide that pixels belong to one group of tissue or to another.
The Color Segmentation is not fine-grained enough as the tissue has non-adjacent colour properties, the Color Deconvolution only allows one continuous ROI to be analysed (yes, I know, I should have one color in the image to find new vectors).

The effect I'm after is a bit like the magic wand selector of Photoshop, where one can shift-click a color or alt-click a colour to respectively add or remove pixels in an image that have certain colour ranges.
The colour ranges I'm thinking of are alreay available in the Display Mode: Histogram of the Color Inspector. Clicking the balls in the 3D cube should ideally be converted to a tissue type selection.

Is such a utility available or could someone give some pointers in this field? http://www.f4.fhtw-berlin.de seems to be off line currently.

Ard
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[Michael Schmid]

Hi Ard,

maybe the Versatile Wand tool plugin may be useful for you?
 
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

To use it, best click at one point with a 'typical' color and then open
the options to try how the parameters should be adjusted (you will get a
preview of the selection)

Michael
________________________________________________________________
On 2016-07-05 13:34, A. Jonker wrote:

> In Fiji we have the Color Inspector 3D, the Cell Counter plugin,
> Color Deconvolution and the Color Segmentation option. I'm looking
> for a combo of these; to interactively decide that pixels belong to
> one group of tissue or to another. The Color Segmentation is not
> fine-grained enough as the tissue has non-adjacent colour properties,
> the Color Deconvolution only allows one continuous ROI to be analysed
> (yes, I know, I should have one color in the image to find new
> vectors).
>
> The effect I'm after is a bit like the magic wand selector of
> Photoshop, where one can shift-click a color or alt-click a colour to
> respectively add or remove pixels in an image that have certain
> colour ranges. The colour ranges I'm thinking of are alreay available
> in the Display Mode: Histogram of the Color Inspector. Clicking the
> balls in the 3D cube should ideally be converted to a tissue type
> selection.
>
> Is such a utility available or could someone give some pointers in
> this field? http://www.f4.fhtw-berlin.de seems to be off line
> currently.
>
> Ard ________________________________
>
> AMC Disclaimer : https://www.amc.nl/disclaimer
>
> ________________________________
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Jerome Mutterer-3]

Kai Barthel's Color Inspector 3D is available from:
http://home.htw-berlin.de/~barthel/ImageJ/ImageJ.htm



On 5 July 2016 at 13:34, A. Jonker <[hidden email]> wrote:
>
> In Fiji we have the Color Inspector 3D, the Cell Counter plugin, Color
Deconvolution and the Color Segmentation option.
> I'm looking for a combo of these; to interactively decide that pixels
belong to one group of tissue or to another.
> The Color Segmentation is not fine-grained enough as the tissue has
non-adjacent colour properties, the Color Deconvolution only allows one
continuous ROI to be analysed (yes, I know, I should have one color in the
image to find new vectors).
>
> The effect I'm after is a bit like the magic wand selector of Photoshop,
where one can shift-click a color or alt-click a colour to respectively add
or remove pixels in an image that have certain colour ranges.
> The colour ranges I'm thinking of are alreay available in the Display
Mode: Histogram of the Color Inspector. Clicking the balls in the 3D cube
should ideally be converted to a tissue type selection.
>
> Is such a utility available or could someone give some pointers in this
field? http://www.f4.fhtw-berlin.de seems to be off line currently.

>
> Ard
> ________________________________
>
> AMC Disclaimer : https://www.amc.nl/disclaimer
>
> ________________________________
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
12, rue du Général Zimmer
67084 Strasbourg Cedex
www.ibmp.cnrs.fr

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[TimFeinstein]

Hi Ard,

Segmenting tissue can be tricky in practice; simple segmentation tools
often have a hard time giving a satisfactory result.  It sounds like your
ideal solution would be a trainable algorithm that uses machine learning
to identify types of tissue.  For example I had an excellent experience
with the Inform software that PE packages with their Vectra pathology
system (no commercial interest).   I believe that you can do something
similar using Trainable Weka Segmentation with Fiji.

Best,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology





On 7/5/16, 7:34 AM, "ImageJ Interest Group on behalf of A. Jonker"
<[hidden email] on behalf of [hidden email]> wrote:

>In Fiji we have the Color Inspector 3D, the Cell Counter plugin, Color
>Deconvolution and the Color Segmentation option.
>I'm looking for a combo of these; to interactively decide that pixels
>belong to one group of tissue or to another.
>The Color Segmentation is not fine-grained enough as the tissue has
>non-adjacent colour properties, the Color Deconvolution only allows one
>continuous ROI to be analysed (yes, I know, I should have one color in
>the image to find new vectors).
>
>The effect I'm after is a bit like the magic wand selector of Photoshop,
>where one can shift-click a color or alt-click a colour to respectively
>add or remove pixels in an image that have certain colour ranges.
>The colour ranges I'm thinking of are alreay available in the Display
>Mode: Histogram of the Color Inspector. Clicking the balls in the 3D cube
>should ideally be converted to a tissue type selection.
>
>Is such a utility available or could someone give some pointers in this
>field?
>https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.f4.fht
>w-berlin.de&data=01%7c01%7ctnf8%40pitt.edu%7ce291464c08384a956c0c08d3a4ca8
>7b9%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=rdhBXr8zKNf6eOp71PvUkDR51
>uIaDav6J%2bd%2fG9hjiq0%3d seems to be off line currently.
>
>Ard
>________________________________
>
>AMC Disclaimer :
>https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fwww.amc.n
>l%2fdisclaimer&data=01%7c01%7ctnf8%40pitt.edu%7ce291464c08384a956c0c08d3a4
>ca87b9%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=IzociploLNmlxgQBDZpicU
>rdibk3oJjDc8T8w0Z%2b2x8%3d
>
>________________________________
>
>--
>ImageJ mailing list:
>https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fimagej.nih
>.gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%7ce291464c08384a956c0
>c08d3a4ca87b9%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=qENvpuGph0WWSEo
>86l76OyH9N3k0UIfPGtHyMRqXlcM%3d

... [show rest of quote]

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