[ome-users] Error to Open .czi File

[Lee Kamentsky]

Hi all,

On Fri, May 15, 2015 at 5:51 AM, William Moore <will at lifesci.dundee.ac.uk>
wrote:

> Hi Ji,
>
> I tried opening with an updated Fiji (Bio-formats 5.1.1 and I see the same
> as you.
> It looks like this is actually a 16-bit image that only contains 8-bit
> data.
> The Original Metadata has:
> BitsPerPixel    8
> PixelType        uint16
>
> Bio-formats is reading the BitsPerPixel incorrectly, since it's setting
> the "SignificantBits" attribute to 16 (see screenshot).
> I've created a ticket to fix this bug:
> https://trac.openmicroscopy.org/ome/ticket/12885
>
>
> Downloading the bioformats package from
> http://downloads.openmicroscopy.org/bio-formats/5.1.1/ and running
> java -jar bioformats_package.jar ZEN\ 2\ Blue\ 8bit.czi
> Seemed to work fine for me.
>
This is issue 25
<https://github.com/CellProfiler/python-bioformats/issues/25> in
python-bioformats. Now that I have the file, I'll test it myself against
bioformats_package 5.1.1 and see if pointing the JVM at that jar fixes the
problem. I'll report back with instructions for launching python-bioformats
with the updated jar if it works. I guess this is a case of data in two
places leading to an unfortunate misinterpretation (8 bits per pixel / data
type 16 bit unsigned). It might make sense for me to check for this
discrepancy and, although technically not my fault, the wise choice is to
favor BitsPerPixel.

The Show Metadata option gave me this (showing SizeC = 1 and SizeT = 1).
>
> <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0"
> Interleaved="false" PhysicalSizeX="0.09999999999999999"
> PhysicalSizeY="0.09999999999999999" SignificantBits="16" SizeC="1"
> SizeT="1" SizeX="256" SizeY="256" SizeZ="1" Type="uint16">
>
>
> Downloading the command line tools from the above url, and running
>
> $ ./showinf ZEN\ 2\ Blue\ 8bit.czi
>
> seemed to open the image fine. With…
>
> Filename = /Users/wmoore/Documents/ZEN 2 Blue 8bit.czi
> Series count = 1
> Series #0 :
> Image count = 1
> RGB = false (1)
> Interleaved = false
> Indexed = true (false color)
> Width = 256
> Height = 256
> SizeZ = 1
> SizeT = 1
> SizeC = 1
> Thumbnail size = 128 x 128
> Endianness = intel (little)
> Dimension order = XYCZT (certain)
> Pixel type = uint16
> Valid bits per pixel = 8
> Metadata complete = false
> Thumbnail series = false
> -----
> Plane #0 <=> Z 0, C 0, T 0
>
>
> Reading pixel data (0-0)
> ************ no LUT for plane #0 ************
> Read 1/1 planes (100%)
> [done]
> 0.121s elapsed (121.0ms per plane)
>
> Launching image viewer
> ….
>
>
> Are these the exact same jars that you downloaded?
> I'm afraid I can't reproduce the problems you're having here and can only
> suggest you try again.
>
>  Hope you can get this working.
> If it still fails to open, please send us any error messages or other info
> that might help to fix this.
>
>  Regards,
>
>   Will.
>
>
>
>
>
> On 15 May 2015, at 07:05, "Tang Ji" <tangji0318 at foxmail.com> wrote:
>
> Dear,
> I have a problem to use bioformats. I've updated my bioformats to its
> latest version 5.1.1. However, when I tried to open my .czi file (1st
> attachment) in ImageJ, it shows that it's a 16-bit image as follows.
> However, the original file is 8-bit image.
> <3006CB03 at F490172D.BD8C5555>
>
> Then I tried to open the .czi file with upgraded Fiji, but it fails
> completely.
> <2803D008 at F490172D.BD8C5555>
>
> What's worse, when I use command "java -jar bioformats_package_5.1.1.jar"
> to open the file, it shows that it contains 2 Z and 2 time points. However,
> it's only a 1-Z and 1-T image.
> <290ACF05 at F490172D.BD8C5555>
>
> Finally, if I use command "java -jar loci_tools.jar", I even cannot open
> the file.
> I'll really appreciate you if you know how to solve the problem. Thanks.
>
> Ji
> May 15, 2015
> <290ACF05 at F490172D.BD8C5555><2803D008 at F490172D.BD8C5555>
> <3006CB03 at F490172D.BD8C5555><ZEN 2 Blue 8bit.czi>
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