Posted by
Kenneth R Sloan on
Jun 03, 2015; 3:21pm
URL: http://imagej.273.s1.nabble.com/Explant-migration-assays-tp5013005p5013026.html
Thanks. I did manage to find that, and it works reasonably well. Right now, I’m struggling with specifying how the overlay and the underlying stack should interact.
Briefly, I want to allow someone to assess co-localization of two signals. One (the stack, conventionally presented as green) has features which are possible CAUSES of certain effects seen in the other (the single image, conventionally presented as blue).
My first, naïve attempt gives me images which are fairly dark - presumably because the blue single image is very dark (but not zero) over most of the image. I probably need to process the blue image into something more like a mask (a simple threshold might do) and present the green stack signal ONLY in the part of the image where the blue signal also exists. Or, perhaps better, present the green signal as BRIGHT when it co-localizes with the blue signal and DIM when it does not. So…turn the blue signal into WHITE above a threshold and GRAY below the threshold and then overlay this 2-level mask on the green stack? [obviously, I want the observer to be able to scroll through the green stack, filtered by the blue signal mask. This looks promising.
That will work when the question is: does the green signal CAUSE the blue signal.
A second question is: are there features revealed in the green signal that BLOCK the blue signal. That may require more thought. I guess I need to talk more to the customer...
Thank you very much for the reply - it was useful.
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.
> On Jun 3, 2015, at 03:34 , Michael Schmid <
[hidden email]> wrote:
>
> Hi Kenneth,
>
> probably the easiest way to have the same overlay for all stack slices is Image>Overlay>Add Image.
>
http://rsb.info.nih.gov/ij/docs/guide/146-28.html#toc-Subsubsection-28.14.2>
> The image used as an overlay can have a lookup table to get a specific color.
> Also the stack can have a LUT. To create e.g. a 'red only' lut, you can use the LUT editor.
>
http://rsb.info.nih.gov/ij/plugins/lut-editor.html>
> Michael
> ________________________________________________________________
> On Jun 1, 2015, at 22:48, Kenneth R Sloan wrote:
>
>> I have an application where I need to overlay a single monochrome image (rendered, say, in Blue), over a monochrome STACK (rendered, say, in Green). All images are the same size in X and Y. I would like to scroll through the stack, and optionally have the ability to modify the blending of the Green and Blue (even simply on/off for the single image would be useful).
>>
>> Is this straightforward? Does anyone have a code snippet to share?
>>
>> Just to make it interesting, I *might* want to annotate the single image (what’s left? - in Red) - but this is not yet absolutely necessary, and I can do without it if it’s difficult.
>>
>> --
>> Kenneth Sloan
>>
[hidden email]
>> Vision is the art of seeing what is invisible to others.
>>
>>
>>
>>
>>> On Jun 1, 2015, at 15:08 , Feinstein, Timothy N <
[hidden email]> wrote:
>>>
>>> Hello,
>>>
>>> I have an assay that seems simple enough to describe, but I cannot find the ImageJ/FIJI tool that quite does what we need. We have tissue explants transferred to a thin collagen gel, and we are measuring migration of cells in um from the edge of the explant. We would automatically detect these nuclei and use, e.g. CellProfiler, but the throughput is not very high and manually marking cells should be faster than troubleshooting a segmenter.
>>>
>>> This seems like it could be addressed with FISH tools - treat the explant as a "nucleus" or simply as a drawn oval and manually mark the nucleus of each migrating cell; the tool would measure the distance of each marked nucleus from the nearest edge of the explant. Can anyone recommend a tool for this job?
>>>
>>> Many thanks,
>>>
>>>
>>> Tim
>>>
>>> Timothy Feinstein, Ph.D.
>>> Research Scientist
>>> University of Pittsburgh Department of Developmental Biology
>>>
>>>
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>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
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