Re: Time Series Flicker Correction

Posted by JimmiB on Jan 29, 2014; 1:29am
URL: http://imagej.273.s1.nabble.com/Time-Series-Flicker-Correction-tp5006250p5006327.html

Hi Jerry,
Thanks for the info, I am guessing that Kota's suggestion is an
implementation of this in image J
*"*




*If you are using Fiji, try "Bleach Correction" and select "Histogram
matching" .Only the current problem is that it takes long time with 16bit
image stack. For 8bit image stack, its pretty fast."*

The problem is that these are dynamic time series, with changes in mean
intensity (due to increased fluorescence and changes in cell size).  This
means that the histogram matching needs to be implemented in a dynamic
manner in that the histogram would need to change slowly with time.



*Dr James Burchfield*
The Garvan Institute of Medical Research
384 Victoria Street
Darlinghurst, NSW, 2010
Australia

Email: [hidden email]
Phone:[phone]
Web: *www.garvan.org.au <http://www.garvan.org.au>*


On Sat, Jan 25, 2014 at 1:40 AM, jerry sedgewick
<[hidden email]>wrote:

> I've done this very effectively, but not in Image J, by histogram matching
> to a target image.  MatLab has code for this, and Photoshop does it as well
> (using an oddly named function called Match Color).
>
> Jerry Sedgewick
>
>
>
> On 1/23/2014 11:40 PM, James Burchfield wrote:
>
>> Hi all,
>> Just wondering if anyone has implemented any "advanced" type of flicker
>> correction.
>>
>> We have image stacks with flicker caused by variation in illumination.
>>  Our
>> approach has been to adjust the image mean towards a local (mean from a
>> number of temporally close images).
>> This works well at a global level, but can make the problem worse in areas
>> of low intensity.
>> Thus a more localised approach may be required
>> eg.
>> http://www.researchgate.net/publication/30995006_A_Block_
>> Smoothing-Based_Method_for_Flicker_Removal_in_Image_Sequences
>> Has anyone implemented this type of approach in imageJ?
>>
>> Cheers,
>> James
>>
>>
>> *Dr James Burchfield*
>>
>> The Garvan Institute of Medical Research
>> 384 Victoria Street
>> Darlinghurst, NSW, 2010
>> Australia
>>
>> Email: [hidden email]
>> Phone:[phone]
>> Web: *www.garvan.org.au <http://www.garvan.org.au>*
>>
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>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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