http://imagej.273.s1.nabble.com/Fwd-possible-bug-in-the-ImageJ-Coloc-2-tp5010830p5010841.html
I'm not sure if it's bug or not. It's certainly possible. But I haven't got
time to look into it. Perhaps Tom has. Perhaps not.
I do remember that we hit a numerical problem. That caused a divide by zero
or something equally bad.... In the case where the mean value of the images
was identical. Unlike in real images but not impossible. The verbose
implementation.might be to do with that. Or that might have been some other
This will allow you to read what we were thinking at the time. Maybe that
I will also have a look to see what we wrote at the time. But do have a
look yourself. It's a good was to see why git is awesome
> Dear Dan,
>
> Thank you for your response! It is the first time that I analyzed the code
> of an open source project, and it is great to get the response from the
> authors of the code.
>
> In the notation that Wikipedia proposed the slope is beta : 0.99. So the
> difference in the slope is 0.99 instead of 1.26, proposed by Coloc2.
> Attached is a plot, showing the difference between two lines -
> comparison.png .
>
> Also I've checked the square error to be sure, and it shows that
> coefficients m and b, given by Coloc 2 plugin are not coefficients of the
> linear regression.
> So there might be a bug in the calculation of the linear regression, or
> you've used the different approach, from the one proposed by Costes in his
> paper.
>
> What to you think?
> I appreciate any possible input from Tom.
>
> Thanks again for your feedback.
>
> Best regards,
> Andrii
>
> ------------------------------------
> Andrii Rogov
> University of Geneva
> GAP - Biophotonics
>
> 22, chemin de Pinchat
> CH-1211 Geneva 4
>
> Phone: +41 22 379 05 66
> Fax: +41 22 379 05 59
>
http://www.gap.unige.ch/biophotonics/>
> On 06/12/2014 15:16, Daniel White wrote:
>
> Hi Andrii
>
> This is interesting. I remember working hard on this part of the maths
> trying to make sure it was right.
>
> Our implementation seems verbose compared to what you suggest from
> Wikipedia. I don't know the reason for that. Perhaps Tom K remembers?
>
> I'm not able to spend time on this sadly
> At least I can't promise.
>
> But perhaps you can investigate where the difference is between the two
> methods. The scatter plot visually suggests that a gradient of close to 3
> is not right. But that's no proof.
>
> That the implementations in scipy and numpy give same answer as you have
> is encouraging. But perhaps we miss something I forgot over time.
>
> The sample image data pixel values are very far from normally distributed.
> So perhaps some assumptions fail.....????
>
> Also I added a large positive offset to both images to simulate data from
> a camera that adds a positive offset. Just to make the threshold algorithm
> struggle harder.... And in fact fail. As a demonstration of why the offsets
> need to be subtracted first. Bit this should not affect a regression or
> correlation calculation???????
>
> cheers, Dan
>
>
http://chalkie.org.uk> ---------- Forwarded message ----------
> From: "Andrii Rogov" <
[hidden email]>
> Date: 5 Dec 2014 17:21
> Subject: possible bug in the ImageJ Coloc 2
> To: <
[hidden email]>
> Cc:
>
> Dear Mr White,
>>
>> I am working on the colocalisation analysis of images and used Costes
>> algorithm implemented in ImageJ Coloc 2 plugin.
>> I've tried to reproduce the results in my python program, but did not
>> succeed.
>>
>> The problem is in calculating linear regression - the first step of
>> Costes algorithm.
>>
>> I found your code on github and after translating java code into python
>> code was able to obtain the same m and b values as calculated in ImageJ.
>> But they are different from values calculated by linear regression
>> expressions proposed by Wikipedia. (
>>
http://en.wikipedia.org/wiki/Simple_linear_regression )
>>
>> Maybe you don't calculate the linear regression, but use some other
>> value... - what is the reason for this?
>>
>> Please find attached 2 tif files (the examples from the Coloc2 webpage),
>> python program, output of the program and a screenshot of ImageJ Coloc
>> output.
>> Software used - ImageJ 1.49g, Python 3.4
>>
>> Channel 1 - red.tif
>> Channel 2 - green.tif
>>
>> Thank you in advance,
>>
>> Best regards,
>> Andrii
>>
>> --
>> ------------------------------------
>> Andrii Rogov
>> University of Geneva
>> GAP - Biophotonics
>>
>> 22, chemin de Pinchat
>> CH-1211 Geneva 4
>>
>> Phone: +41 22 379 05 66
>> Fax: +41 22 379 05 59
>>
>>
http://www.gap.unige.ch/biophotonics/>>
>>
>