http://imagej.273.s1.nabble.com/Histogram-scale-change-when-importing-ZVI-files-tp5008753p5008763.html
> Thank you for the reply. A follow-up question:
> If my min. also varies, what does this mean?
> I have a few images here with min.'s of 7552, 5888 and max. of 65520. Opening without bio-formats results again in a 0-65535 distribution. The histograms reflect this with the "0-65535" image skewing more to the center, whereas the other image skews to the left.
> I'd like to bin all my images equivalently to get a distribution of intensities at a given bins. This is why I'm concerned that right now, my images are not comparable.
Run the Histogram command by pressing alt+h, enter 0 as "X min", 65536 as "X max" and you will get a histogram that uses a bin size of 256. The 0 and 65536 values are remembered so they only have to be entered the first time you press alt+h.
> What do you think?
>
>
> Jorge
>
>
> Sent from my iPhone
>
> On Jul 15, 2014, at 16:15, "G. Esteban Fernandez [via ImageJ]" <
[hidden email]<mailto:
[hidden email]>> wrote:
>
> The histogram display is being scaled to the max. intensity present in the
> image. Try this: open an image that gives you a scale <65,535 and display
> the Histogram like you have been doing, then draw one pixel of intensity
> 65,535 anywhere in the image using the pencil tool, then display the
> Histogram again. The scale should change from <65,535 to 65,535.
>
> Bio-Formats is not changing the image, so any subsequent analysis is
> comparable between images that have different histogram scales.
>
> -Esteban
>
>
> On Tue, Jul 15, 2014 at 11:33 AM, javila0624 <[hidden email]</user/SendEmail.jtp?type=node&node=5008756&i=0>> wrote:
>
>> Hello all,
>> I'm having a difficult time understanding why histogram scales change when
>> I
>> import .zvi using the bio-formats importer. I'd like to convert all of my
>> files to .tif format and use ImageJ for analysis but I am concerned any
>> subsequent analysis will not be valid as a result of this rescaling.
>>
>>
>>
>> Here's what I have done:
>> I save a 16-bit .zvi file and load onto Mac OSX. (I know it is 16-bit
>> because my Axiovision camera captures at this depth and the software
>> confirms in the file information.)
>> Using the bio-formats import option, I open the 3-channel .zvi file with
>> the
>> Standard-ImageJ stack option selected. The 3 channels are split;
>> autoscaling
>> is off, and color mode is in gray-scale. I have also tried different
>> variations of this by using hyperstack options, and color-mode on default.
>>
>> The result has been the same: Upon clicking on the histogram function, I
>> see
>> that instead of seeing a 0-65535 range on my intensity distribution scale,
>> images from both different channels and different samples can vary in the
>> intensity scaling. Example: sample 1, channel 1 shows a 0-65520 scale;
>> sample 1 channel 3 shows a 0-65520 scale ;sample 2, channel 1 shows a
>> 0-65520 scale; sample 2, channel 3 shows a 0-58890 scale.
>>
>> In an attempt to confirm that the images should be on a 0-65535 scale,
>> opening the files without bio-formats importer and then clicking on the
>> histogram function shows me that this is in fact the case: the scale is
>> 0-65535. (this is not an option for me however, as images areas are
>> scrambled on the ImageJ window, i.e. the image quadrants/relative positions
>> are 'scrambled' on the image.)
>>
>> It seems like a straightforward scaling or binning problem, but how can the
>> importer be set to bin equivalently?
>>
>>
>> Can anyone help me understand why this happens? How can I maintain the
>> 16-bit scale (0-65535)?
>>
>> I've played around with converting to 32-bit and re-converting back to
>> 16-bit. I'd rather avoid this step if at all necessary and retain the
>> original data scale.
>>
>>
>> Thank in advance for any help!!
>>
>>
>>
>>
>>
>> --
>> View this message in context:
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http://Nabble.com>.
>>
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