ImageJ question

[Mike Tighe]

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would anybody know if it is possible to import a 3 or 4 color image into imageJ and have the software locate cells or objects that have signal in all or some of those channels? For example I have one channel for CD8 Tcells and I would like to have the software show me which of those CD8's are positive in one or two other channels. Rather than doing this manually.

Thanks for any help!!
Mike

[Zdenek Svindrych-2]

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Hi Mike,
no one would dare to state that ImageJ cannot solve particular image
processing problem. So the answer is: Yes, it is possible. There are
thousands plugins available, and if you're really short of luck, you can
always write your own plugin...

If your staining is really perfect and your images of great quality (I
assume widefield images of a monolayer of cells), so you can reliably
threshold individual positive cells in all channels, you can then multiply
the masks (logical AND operation) and analyse the results. ROI Manager and
Macro Recorder can be very helpful for you.

Alternatively, you can threshold individual cells and measure their
'colors', that is averages from all channels. You then can build a set of
rules to classify individual cells (something like image-based cytometry).
But unless you have hundreds of cells per image or you're good with macros,
manual approach is usually faster...

Good luck!

zdenek



---------- Původní zpráva ----------
Od: Mike Tighe <[hidden email]>
Komu: [hidden email]
Datum: 30. 6. 2015 15:43:43
Předmět: ImageJ question

"*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

would anybody know if it is possible to import a 3 or 4 color image into
imageJ and have the software locate cells or objects that have signal in all
or some of those channels? For example I have one channel for CD8 Tcells and
I would like to have the software show me which of those CD8's are positive
in one or two other channels. Rather than doing this manually.

Thanks for any help!!
Mike"

[Cameron, Lisa]

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There is an Image J listserv.
I would recommend posting your question there: ImageJ Interest Group [[hidden email]]

Cheers,
Lisa

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Mike Tighe
Sent: Tuesday, June 30, 2015 10:38 AM
To: [hidden email]
Subject: [CONFOCALMICROSCOPY] ImageJ question

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*****

would anybody know if it is possible to import a 3 or 4 color image into imageJ and have the software locate cells or objects that have signal in all or some of those channels? For example I have one channel for CD8 Tcells and I would like to have the software show me which of those CD8's are positive in one or two other channels. Rather than doing this manually.

Thanks for any help!!
Mike


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[Julio Vazquez-2]

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You might also want to consider Cell Profiler, which may make the task a bit easier. The software is available, and you may be able to use some of their example pipelines (such as Cell/particle counting and scoring the percentage of stained objects) with just some modifications.

Julio.
--



Julio Vazquez
Fred Hutchinson Cancer Research Center
Seattle, WA 98109

http://sharedresources.fhcrc.org/core-facilities/scientific-imaging



On Jun 30, 2015, at 7:37 AM, Mike Tighe wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> would anybody know if it is possible to import a 3 or 4 color image into imageJ and have the software locate cells or objects that have signal in all or some of those channels? For example I have one channel for CD8 Tcells and I would like to have the software show me which of those CD8's are positive in one or two other channels. Rather than doing this manually.
>
> Thanks for any help!!
> Mike

[Pongor Csaba]

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Dear Mike!

Solving the problem should be possible using imageJ. ImageJ has several segmentation plugins that can be used to locate cells/objects if one has the objects are found one has to be look for colocaliyation in the different channels. The question is whether to use 2D or 3D data as the segmentation tools are different (Analyze particles/ROI manager for 2D and 3d Objest counter/3D ROI manager for the other. This depends on the available images and on the biological problem eg. size of the objects expected distribution etc.. Using some macro programming the problem should be fairly easy.

I am working on a similar problem in 3D so I can keep you posted on how it is going on!

Yours, Csaba Pongor

Nikon Center of Excellence
Institute of Experimental Medicine
Hungarian Academy of Sciences




----- Eredeti üzenet -----
Feladó: "Mike Tighe" <[hidden email]>
Címzett: [hidden email]
Elküldött üzenetek: Kedd, 2015. június 30. 16:37:51
Tárgy: ImageJ question

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*****

would anybody know if it is possible to import a 3 or 4 color image into imageJ and have the software locate cells or objects that have signal in all or some of those channels? For example I have one channel for CD8 Tcells and I would like to have the software show me which of those CD8's are positive in one or two other channels. Rather than doing this manually.

Thanks for any help!!
Mike

[Michael Model]

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Hello Mike,
You can do this for example by selecting all the cells positive for CD8
and use "redirect measurements" (in Analyze-Set Measurements) to the other
channels. This way you chose the area based on the CD8 channel but measure
the cells in other channels.

Mike Model

On Tue, Jun 30, 2015 at 10:37 AM, Mike Tighe <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> would anybody know if it is possible to import a 3 or 4 color image into
> imageJ and have the software locate cells or objects that have signal in
> all or some of those channels? For example I have one channel for CD8
> Tcells and I would like to have the software show me which of those CD8's
> are positive in one or two other channels. Rather than doing this manually.
>
> Thanks for any help!!
> Mike