http://imagej.273.s1.nabble.com/Phase-contrast-image-segmentation-for-counting-fibroblasts-tp5023774p5023776.html
I do not understand what you mean by stitched. It looks as if the cellular
the image. The darkening is in the center only indicating that the image is
Am Di., 28. Juli 2020 um 18:09 Uhr schrieb Straatman, Kees (Dr.) <
> Dear sfreema1,
>
> To improve your image you can use a Gaussian Blur filter
> (Process>Filters>Gaussian Blur...) of 8 and divide your image with the
> filtered image using the image calculator (Process>Image Calculator...).
> The macro code below will do the same on an open image
>
> title = getTitle();
> run("Duplicate...", "title=filter");
> run("Gaussian Blur...", "sigma=8");
> imageCalculator("Divide create 32-bit", title,"filter");
> selectWindow("Result of A12_-1_1_1_Stitched[Phase_Contrast]_001.tif");
>
> You can play around with the type of filter or filter settings to see if
> you can get a better result.
> I don't think you really will be able to count the number of cells (others
> might have better ideas) but it might be possible to collect information
> about the area covered by cells using the Labkit plugin -
>
https://imagej.net/Labkit>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
>
> Advanced Imaging Facility
>
> University of Leicester
> www.le.ac.uk/advanced-imaging-facility<
>
http://www.le.ac.uk/advanced-imaging-facility>
>
> ________________________________
> From: sfreema1 <
[hidden email]>
> Sent: 28 July 2020 13:47
> Subject: Phase contrast image segmentation for counting fibroblasts
>
> Good morning,
>
> I am trying to find a workflow for counting cells in a phase contrast
> image.
> These are fibroblasts that I grew in a 96-well plate. Several images were
> stitched together.
>
> As I look through other similar questions here and elsewhere, I find a lot
> of the examples are geared towards more circular cells. I have tried using
> the common workflow (thresholding/binarizing -> analyze particles) but I
> have not been content with my results.
>
> Because the images were taken in the 96-well plate, all my phase contrast
> images have a feature where the centers of the wells are darker and have
> more contrast, while as I move away from center, the features brighten and
> lose contrast.
>
> I found that Sharpen->Find Edges was helpful in outlining the cells and
> apparently removing the uneven illumination, but then I have not been able
> to proceed from there.
>
> I feel another issue with these cells is that they crowd very closely
> together, and I think it is hard to distinguish two separate cells even by
> eye sometimes.
>
> I would appreciate insight anyone has to give. I have attached a sample
> image below from my dataset. A12_-1_1_1_Stitched[Phase_Contrast]_001.tif
> <
>
https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2Ffile%2Ft382700%2FA12_-1_1_1_Stitched%255BPhase_Contrast%255D_001.tif&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C08c703362faf4bf6278a08d832f68dcc%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637315381818990765&sdata=yfNiHKkzoHm%2BKIwrBAAd9ZyLs50UeaqT2SwuUax9O00%3D&reserved=0> >
>
>
>
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