http://imagej.273.s1.nabble.com/Re-IMAGEJ-Digest-25-Feb-2015-to-26-Feb-2015-2015-67-tp5011805p5011848.html
Micro-Manager. Currently the code [1, 2] is working well but it's
Université de Toulouse - Bât. 4R3B1
> Hi,
>
> Thanks for your explanation about performance.
> At the moment, I’m stuck with the fact that I want to compute correlation along !D only, while as far as I understand, most function accessible from the gui compute 2D fft and/or correlations. I guess I’ll have to use the built-in 1D FHT you mentioned; since I’m not familiar with the API, a minimal example of how to (i) reshape m x n x l 3D-stack to a (mxn) x l 2D-stack and (ii) compute fft or fht along the with of the new image would be really helpful…
>
> Thank you very much for your help. Best,
>
> Thomas
>
>
> Le 27 févr. 2015 à 12:08, Michael Schmid <
[hidden email]> a écrit :
>
>> Hi Thomas,
>>
>> if you don't use a macro to loop over all pixels of an image or the like, there won't be a significant difference in performance. Just don't do any time-consuming operations in a macro.
>> E.g., an FFT is not any slower when called from a macro than when called from Java code.
>>
>> To avoid the overhead of displaying temporary images in a macro, use BatchMode.
>>
>> Michael
>> ________________________________________________________________
>> On Feb 27, 2015, at 12:03, Thomas Julou wrote:
>>
>>> Hi Michael,
>>>
>>> Thank you very much for taking time to look at my question. What you propose is very close to what I’d be able to come up with by myself. I posted on this mailing list specifically because my impression was that this macro-like approach would yield very low performance. And so far my experience was that it’s difficult to incrementally improve code written in this way…
>>>
>>> So let’s rephrase my question: should I expect a large jump in performance between a macro-like plugin and calling appropriate APIs directly? If yes, which ones? (cf my previous post…)
>>>
>>> Best,
>>> Thomas
>>>
>>>
>>> Date: Thu, 26 Feb 2015 17:37:19 +0100
>>> From: Michael Schmid <
[hidden email]>
>>> Subject: Re: Help with computing correlations along z in stacks.
>>>
>>>> Hi Thomas,
>>>>
>>>> unfortunately I don't know matlab, but it seems to my that you can it in ImageJ without very much programming, i.e., in a macro:
>>>> - Image>Stacks>Reslice to have the z direction run in x or y.
>>>> - Convert to float and subtract the background value, so that the background gets a value of 0
>>>> - Pad the canvas size to a square that is a power of 2.
>>>> - Create a 32-bit image of the same size with you function centered in the middle, running in the same x or y direction as the original z direction, only in the middle line.
>>>> - For all stack slices, run Process>Math>FD Math and correlate (with inverse transform) the images of the resliced stack with the image having the function.
>>>> - Combine the output images to a stack, and reslice to the original orientation if desired.
>>>>
>>>> If you want to do programming in Java, you could also use the built-in 1D FHT (fast Hartley transform) of ImageJ.
>>>>
https://github.com/imagej/imagej1/blob/master/ij/process/FHT.java>>>> Correlation is simply multiplying the FHT arrays index by index, then transform back (inverseTransform1D).
>>>>
>>>>
>>>> Michael
>>>> ________________________________________________________________
>>>>
>>>>
>>>> On Feb 26, 2015, at 12:14, Thomas Julou wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I hope this list is the right place to ask my question.
>>>>> In order to achieve robust segmentation of bacteria from white light pictures, we use a "correlation" image. The principle is to acquire a z-stack of bright field pictures, and to correlate the intensity along z with an « expected" intensity profile. So far, we wrote the code in Matlab only.
>>>>>
>>>>> However for several purpose, I’d be interested in having the code written for imageJ (among other, doing the acquisition with micro-manager and processing images on the fly; though I know I could call MM from Matlab). Since I'm new to plug-in programming (but anticipate that speed will matter in this case), I'd really appreciate getting pointers to appropriate libraries / examples.
>>>>>
>>>>> Here are a few specific questions:
>>>>> - is it better to run a FFT per (x, y) intensity profile or is there any kind of "vectorized syntax"?
>>>>> - which fft library do you recommend? fftw? imglib2?
>>>>> - is it realistic to write this for cuda / opencl already? (to me it looks like a good task for a gpu)?
>>>>>
>>>>> Below is the code I wrote for matlab since it might help to answer.
>>>>> Thank you in advance for your help. Best,
>>>>>
>>>>> Thomas
>>>>>
>>>>> --
>>>>> Thomas Julou | Computational & Systems Biology | Biozentrum – University of Basel | Klingelbergstrasse 50/70 CH-4056 Basel | +41 (0)61 267 16 21
>>>>>
>>>>>
>>>>>> function IM_CORREL = correlImg(IM, sigma)
>>>>>> [ny, nx, nz] = size(IM);
>>>>>> z = (1:nz)';
>>>>>> center = round(nz/2);
>>>>>>
>>>>>> zProfile = - (z-center) .* exp(- (z-center).^2 / (2*sigma^2));
>>>>>> zProfileFFT = fft(zProfile);
>>>>>> zProfileFFT(1) = 0;
>>>>>>
>>>>>> zProfileFFTc = conj(zProfileFFT);
>>>>>> Z_PROFILE_FFT_C(1,1,:) = zProfileFFTc;
>>>>>> Z_PROFILE_FFT_C = repmat(Z_PROFILE_FFT_C, [ny nx]);
>>>>>>
>>>>>> IM_Z_FFT = fft(IM, [], 3);
>>>>>> IM_Z_FFT(:,:,1) = 0;
>>>>>> CORREL = real(ifft(IM_Z_FFT.*Z_PROFILE_FFT_C, [], 3));
>>>>>>
>>>>>> idx = [center+1:nz 1:center];
>>>>>> IM_CORREL = CORREL(:,:,idx);
>>>>>
>>>>> --
>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>
>>>
>>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html