http://imagej.273.s1.nabble.com/Problems-using-the-FFT-Bandpass-Filter-tp5012174p5012225.html
>>>> On Mar 25, 2015, at 18:08, Hening Bettermann wrote:
>>>>
>>>> Hi!
>>>>
>>>> I am looking for a way to extract regions of equal degrees of blur from 16 bit TIF RGB images...
>>>>
>>>> Process > FFT > Bandpass filter, with 2 different settings: 1-0 and 16-0.
>>>>
>>>> ... In ImageJ, both of the resulting images look like the complete image, just in black and white
>
>>> On 27 Mar 2015, at 10:39h, Michael Schmid wrote:
>>>
>>> Hi Henning,
>>>
>>> the following works for me:
>>>
>>> run("HeLa Cells (1.3M, 48-bit RGB)");
>>> run("Stack to RGB");
>>> run("Bandpass Filter...", "filter_large=16 filter_small=0 suppress=None tolerance=5");
>>> run("16-bit");
>>>
>>> Make sure that you have selected "automatic" 16-bit display range in Edit>Options>Appearance. Otherwise, a 16-bit image will appear black if it has low pixel values.
>>> I don't see a reason for using 16-bit resolution, however; RGB has only 8 bits, so 8 bits would give the same result.
>>> It would make sense to convert to 32 bits (floating point) *before* the Bandpass Filter is applied; just make sure you always use the same settings in Edit>Options>Conversions (if the color channels have roughly equal noise, 'weighted RGB conversions' should be off).
>>>
>>>
>>> Michael
>
>> On Mar 27, 2015, at 17:33, Hening Bettermann wrote:
>> --------------------------------------------------
>> Hi Micheal,
>> thank you for your reply! -
>> My preferences (Edit > Options) are configured the way you describe. Yet, the 16 bit files look all black. -
>> Where do I find the 'HeLa Cells' command? The Find-command did not find it anywhere in any menu in Help > Documentation. 'Run' may sound like it has to be run from the command line, but all the others are menu commands.
>> Kind regards - Hening.
>>
>> Add-on:
>> Unlike what I wrote in my first mail, I still get 'out of memory' alerts. I had overlooked them, since they are covered by new frames that open.-
>> ImageJ 2.0 has just been released. Should I install that?
>
> Hi Henning,
>
> "HeLa Cells" is in the "Open Samples" directory, just to have a test image.
> If you get an 'out of memory' error, maybe you have a large virtual stack? After processing the images, they must be all in memory. In that case, open the stack slices one by one and save the results into a separate directory.
>
> But I noticed now that the Bandpass Filter does not work as expected for the RGB images; you should convert from RGB to 32 bits before running the Bandpass Filter. Also the analysis steps following the Bandpass for that purpose would be best done with 32 bits (background subtraction, taking the absolute value, some blurring). Then select a reasonable grayscale range and convert to 16 bit (Edit>Options>Scale when converting should be on).
>
> ---
> If 16-bit images look black in a program different than ImageJ, it might indicate that (a) that program does not read them correctly or (b) that program scales 0-65535 to black-white, but the pixel values are much smaller (e.g. 0-255), so they all appear black.
>
> I am using ImageJ 1.49p. I don't know much about ImageJ 2, but I don't think it would be better.
>
> Michael
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlI have in the meantime tried to read some of the documentation, but without being able to extract much of use for my purpose.
Strange enough, if I first convert to RGB stack (Image > Color > Stack to RGB), then convert to 32 bit grayscale (Image > Type > 32 bit), then export as TIF and open that in Preview, I see an inverted image, not just black.
Regardless, trying to run Process > FFT > Bandpass Filter, still gives me the memory error. - Which operating system and version do you use? How much RAM do you have/allocated to ImageJ?