CZI to tiff Scaling problem

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CZI to tiff Scaling problem

Kira Rienecker
Hello everyone!


I've been using DSRichardson's czi to tiff conversion macro for Image J Bioformats and one particular file is giving me problems with scaling. All of the settings for pixel size seem to be correct (0.441 µm^2 per pixel), but the measurements are coming out ~1/4 the size they should be.


I haven't had this problem with ANY of the other files from the same scan day (Zeiss Axioscan) and I have scanned this slide alone on a separate day and I still get the same result.


Any ideas?

I appreciate the help!


-Kira Rienecker

Final year PhD student

(MacBook Pro user)


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Re: CZI to tiff Scaling problem

Douglas Richardson
Hi Kira,

I think I know what's wrong.  If you open the original .CZI file in ZEN and
click on the info tab to the left of the image you should find the total
number of pixels in the X and Y axes. Write these down.

Next go back to the .tif file you created and open it in Fiji/ImageJ and
click on the Image<Properties tab.

Is the total number of pixels the same? I suspect it's reduced.

If the total number of pixels (in X and Y dimensions) is incorrect, the
macro probably converted the wrong resolution level from the .CZI pyramid
file.

Unfortunately I hard-coded this and have since discovered that ZEN varies
the number of resolution levels based on the size of the image.  If you
just use Plugins<Bio-Formats<Bio-Formats Importer to open the one .CZI file
that converted incorrectly, a number of thumbnails should appear
representing the different resolution levels.  Just open the one with the
most pixels (should be the top one) and save it as a .tif.

-Doug


On Tue, Jul 31, 2018 at 4:51 AM, Kira Rienecker <[hidden email]>
wrote:

> Hello everyone!
>
>
> I've been using DSRichardson's czi to tiff conversion macro for Image J
> Bioformats and one particular file is giving me problems with scaling. All
> of the settings for pixel size seem to be correct (0.441 µm^2 per pixel),
> but the measurements are coming out ~1/4 the size they should be.
>
>
> I haven't had this problem with ANY of the other files from the same scan
> day (Zeiss Axioscan) and I have scanned this slide alone on a separate day
> and I still get the same result.
>
>
> Any ideas?
>
> I appreciate the help!
>
>
> -Kira Rienecker
>
> Final year PhD student
>
> (MacBook Pro user)
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html