http://imagej.273.s1.nabble.com/Feature-description-of-condensation-tp5022129p5022136.html
What I've finally computed is the *global* StdDev, i.e. that of the
sample images as such (no ROIs or subregions) and that's pretty simple.
> Hi Thomas,
>
> you should surely follow the suggestions from the others on using higher order texture descriptors for the analysis. I just want to add a comment: if you observe some factors that interfere with your analysis, try to adapt the analysis accordingly. Don't expect that more sophisticated methods necessarily compensate for those intensity fluctuations.
> Since the intensity fluctuates in a single cell, you could reduce the scale of the analysis to a smaller size, excluding clear outliers. Additionally, you could use a more robust statistics.
> Using your data as an example, for each image I measured the coefficient of variation on 32 subregions randomly extracted from the cells (radius=20 pixels, arbitrary chosen), excluding only the most obvious nucleoli. Since the distribution of the measurements was not approximating a Gaussian, I took the median. The result is a coefficient of variation of 0.21 and 0.17 for the 'aggregate' and 'smooth' images, respectively, with a dispersion of 0.02 (median absolute deviation). This is why I suggested to try such a simple approach, before going for more complex approaches.
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Lendl,Thomas
> Sent: Freitag, 26. April 2019 12:25
> To:
[hidden email]
> Subject: Re: Feature description of condensation
>
> Hi Giovanni,
>
> Thank you for the suggestion! I already tried that and there are differences in CV but not so pronounced. Both types show coarser intensity fluctuations (due to nucleoli and uneven intensity) that mess up the standard deviation.
>
>
> -----Original Message-----
> From: ImageJ Interest Group <
[hidden email]> On Behalf Of Cardone, Giovanni
> Sent: Freitag, 26. April 2019 11:38
> To:
[hidden email]
> Subject: Re: Feature description of condensation
>
> Hi Thomas,
>
> if you limit the analysis to just the protein content, a simple coefficient of variation, aka relative standard deviation, of the intensity should already be able to highlight the difference in a numerical manner.
>
> I hope it helps.
> Giovanni
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Lendl,Thomas
> Sent: Freitag, 26. April 2019 11:17
> To:
[hidden email]
> Subject: Feature description of condensation
>
> Dear all,
>
> I need to quantify the amount of aggregation of a certain protein in nuclei. Visually the difference is obvious but how to put that into numbers? I thought about some kind of wavelet analysis since the fluctuations in the aggregated state have a different frequency but I didn't find the right tool or the right parameters. Has anybody encountered a similar problem?
>
>
https://www.dropbox.com/sh/jknltkw2jmyeg1x/AAApo_VMu2-fe3ssvxZJXZu3a?dl=0>
> Best regards,
> Thomas
>
> ………………………………..
> Thomas Lendl
> Image Analysis/FACS Specialist
>
> IMP
> Research Institute of Molecular Pathology Campus-Vienna-Biocenter 1
> 1030 Vienna, Austria
>
>
>
>
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