> Esteban,
> 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.
> This was done using the same steps as mentioned on my post.
>
> 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.
>
>
> 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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