http://imagej.273.s1.nabble.com/measuring-grayscale-of-objects-in-a-plate-tp5004160p5004167.html
Centroid coordinates of any ROI (1 and 2) are coordinates of your plate image. Sorting in y means that you can group the "lines" and sorting in x allows to group the "columns". Each well covers a box in which the related roi coordinates are falling, if not, than the roi is not inside the well. Where is the problem?
> I am confused about what "your ROIs" means. Do you mean 1) the ROI set that
> I have saved, which has one ROI for each of the 48 wells, or 2) the ROIs
> that I get after I threshold/analyze particles/save to ROI manager?
>
> If you mean (1), my saved ROI set has ROIs that includes each well in its
> entirety. However, since seeds take up only a fraction of the well, and
> since seeds can be in many different shapes and sizes and places within the
> well, my ROI set doesn't actually help very much in identifying the seeds
> themselves. In my original post, I suggested that if I could apply the
> threshold/analyze particle functions to only the ROI and not the entire
> image, then I could apply the process 48 times, one time for each ROI/well,
> which would then be in order, since my ROI set is already in order, and I
> do this in the order of my ROI set. However, I do not know how to apply the
> functions to only the ROI, so I can't use this method (unless you know how
> to do it).
>
> If you mean (2), the seeds vary in position within each well. So even
> though in theory, if I tell the program to list in increasing y-coordinate
> values and then in increasing x-coordinate values, I should get the
> wells/seeds in order, this is not the case in practice. This is what I
> tried to explain in my previous post. Unless I am misunderstanding you, in
> which case you would have to explain your method in slightly more detail.
>
> Thanks
>
> JDing
>
>
> On Fri, Jul 26, 2013 at 4:09 PM, Karsten Rodenacker-3 [via ImageJ] <
>
[hidden email]> wrote:
>
>> Assuming your wells build a chequerboard and the image is aligned with it,
>> the coordinates of your ROIs will allow the ordering of the results. Of
>> course the actual list of result entries depend on the sequence of your
>> ROIs in the ROI manager rspw. on the first found pixel per region.
>>
>> Possibly you have to load the results into Excel or R for the ordering in
>> x and y.
>>
>> Regards
>> Karsten
>>
>> Am 26.07.2013 um 22:55 schrieb JDing <[hidden email]<
http://user/SendEmail.jtp?type=node&node=5004164&i=0>>:
>>
>>
>>> You understand me correctly, but your suggestion doesn't seem to work. I
>>> added "center of mass" to the measurements and it didn't put the wells
>> in
>>> order. Here is my explanation: even though the sides of my plate are
>> aligned
>>> with the x and y axes, the seeds themselves vary in their position
>> within
>>> the well (and their size). So the seed in A1 could be centered at
>> coordinate
>>> (50, 50), while B1 is at (100, 49), and C1 is at (150, 49.5), etc. In
>> this
>>> case, if ImageJ measured/listed in order of increasing y-coordinate (the
>>> default for my computer), it would list B1 and C1 before A1. So this
>> method
>>> doesn't work well in real practice.
>>>
>>> Thank you for your consideration, though.
>>>
>>> JDing
>>>
>>>
>>>
>>> --
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>> Karsten
>> [hidden email] <
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