Fwd: automatic detection out-of-focus images

["F.Xavier Gómez"]

Dear all,

And the plugin GM-Autofocus.java ?

http://svg.dmi.unict.it/iplab/imagej/Plugins/Autofocus/gmautofocus.htm

I used it  to select my best focus plane with my stack of fluorescence pictures.

Best Regards,

F.Xavier

> El 14/03/2011, a las 18:05, Gabriel Landini escribió:
>
>> On Monday 14 Mar 2011 15:49:25  Baron, Ken (US SSA) wrote:
>>> Just compress your images with jpeg or probably any image compressor. The
>>> file that is the largest is probably the one with best focus.
>>
>> That would only work if all the images were of the same scene which is not the
>> case here.  A "busy" image out of focus may well take more space to store
>> compressed than one with very few objects but well in focus.
>> This would not work either when parts of the image are in focus and others are
>> not.
>> Rather than compressing the image, it would be better to look at the high
>> frequencies (for example in the Fourier space), but even so, this makes sense
>> only when you compare images of the same (or very similar) scene. This would
>> fail when the image is originally lacking high frequency components.
>>
>> Anyway, finding the best focused image requires looking how much focus can be
>> achieved at other focal distances. The eye does it and photo cameras do it
>> that way too.
>> Have a look at various papers on autofocus techniques (which search for the
>> best focused image) to get an idea how these things are implemented.
>> Understanding the technical problem might help realising what can and cannot
>> be achieved under certain constraints.
>>
>> Roca X, Binefa X, Vitria J. New autofocusing algorithm for cytological tissue
>> in a microscopy environment. Optical Engineering 1998;37(2):635-641.
>>
>> Firestone L, Cook K, Culp K, Talsania N, Preston K. Comparison of autofocus
>> methods for automated microscopy. Cytometry 1991;12:195-206.
>>
>> Santos A, Ortiz de Solorzano C, Vaquero JJ, Pena JM, Malpica N, Del Pozo F.
>> Evaluation of autofocus functions in molecular cytogenetic analysis. Journal
>> of Microscopy 1997;188(3):264-272.
>>
>> Pieper RJ, Korpel A. Image processing for extended depth of field. Applied
>> Optics 1983;22(10):1449-1453.
>>
>> I hope this is useful.
>> Regards
>>
>> Gabriel
>

[Crowell Elizabeth]

Hello ImageJ community,

Thank you all for your many responses.  I think I have a good lead on a
solution now (see below)...

My goal is to identify out-of-focus images in image sets produced by
scanning a slide.  Each image represents a different field of view, and
is 2D.
I have measured intensity, standard deviation, integrated density, etc
on DAPI images processed using Find Edges + thresholding, and I come
close to being able to discriminate out-of-focus and in-focus images,
but alas, no cigar!  The distributions overlap too much, and the means
vary from one experiment to the next.

Dan White suggested trying a module in CellProfiler called
MeasureImageQuality.  Indeed, this gives me the best results I have
found so far, using a criterion that corresponds to the slope of the
log-log magnitude spectrum.  The distributions of slope values are
well-separated and the 95% confidence intervals show little overlap.  
Furthermore, the mean seems to vary little from one experiment to the next.
Since all my processing and analysis is in ImageJ so far, I would like
to be able to compute the slope of the log-log magnitude spectrum in ImageJ.

 From what I could tell after an Internet search, this is a tool used
frequently in acoustics.  So I hope one of the acoustics specialists out
there knows how to compute the slope of the log-log magnitude spectrum
in ImageJ!

Kind Regards,
Elizabeth

> F.Xavier Gómez a écrit :
>  
>> I used it  to select my best focus plane with my stack of fluorescence pictures.
>>    
> This is not quite what I need to do:  I am not working with stacks,
> but a collection of 100 single images of different fields of view.  I
> am not interested in selecting the best image, but in discarding the
> defective images, of which there may be 100 or zero.  Thank you for
> the link, though, which I think I can use for other applications!
> Best Regards,
>
> F.Xavier
>
>
>  
>> El 14/03/2011, a las 18:05, Gabriel Landini escribió:
>>
>>    
>>> On Monday 14 Mar 2011 15:49:25  Baron, Ken (US SSA) wrote:
>>>      
>>>> Just compress your images with jpeg or probably any image compressor. The
>>>> file that is the largest is probably the one with best focus.
>>>>        
>>> That would only work if all the images were of the same scene which is not the
>>> case here.  A "busy" image out of focus may well take more space to store
>>> compressed than one with very few objects but well in focus.
>>> This would not work either when parts of the image are in focus and others are
>>> not.
>>> Rather than compressing the image, it would be better to look at the high
>>> frequencies (for example in the Fourier space), but even so, this makes sense
>>> only when you compare images of the same (or very similar) scene. This would
>>> fail when the image is originally lacking high frequency components.
>>>
>>> Anyway, finding the best focused image requires looking how much focus can be
>>> achieved at other focal distances. The eye does it and photo cameras do it
>>> that way too.
>>> Have a look at various papers on autofocus techniques (which search for the
>>> best focused image) to get an idea how these things are implemented.
>>> Understanding the technical problem might help realising what can and cannot
>>> be achieved under certain constraints.
>>>
>>> Roca X, Binefa X, Vitria J. New autofocusing algorithm for cytological tissue
>>> in a microscopy environment. Optical Engineering 1998;37(2):635-641.
>>>
>>> Firestone L, Cook K, Culp K, Talsania N, Preston K. Comparison of autofocus
>>> methods for automated microscopy. Cytometry 1991;12:195-206.
>>>
>>> Santos A, Ortiz de Solorzano C, Vaquero JJ, Pena JM, Malpica N, Del Pozo F.
>>> Evaluation of autofocus functions in molecular cytogenetic analysis. Journal
>>> of Microscopy 1997;188(3):264-272.
>>>
>>> Pieper RJ, Korpel A. Image processing for extended depth of field. Applied
>>> Optics 1983;22(10):1449-1453.
>>>
>>> I hope this is useful.
>>> Regards
>>>
>>> Gabriel
>>>      

--

Elizabeth CROWELL

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Institut Pasteur
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