[ome-users] ome-users Digest, Vol 122, Issue 17

Wed May 20 13:15:35 BST 2015

Hi Ji,

Thanks for the extra information.
 I've added it to the ticket at http://trac.openmicroscopy.org/ome/ticket/12885.
It won't be me fixing that bug, but when it is worked on you may be contacted for more info if we need it.

 Thanks,

  Will.

On 17 May 2015, at 13:33, Tang Ji <tangji0318 at foxmail.com> wrote:

> Dear Will,
> Thanks for your help.
> The interesting thing is that when there are several other .czi files under a folder, the error will recur. You can try to open a .czi file after you unzip the attachment, and then you'll get what I find.
> I tested several versions of bioformats, and I found that the error exists from version 5.0.7 to 5.1.1. However, version 5.0.6 to 5.1.0-m3 is fine.
> I hope the information will make me understood. Thanks again.
> 
> Ji
> May 17, 2015
> 
> 
> ------------------ Original ------------------
> From:  "ome-users-request";<ome-users-request at lists.openmicroscopy.org.uk>;
> Date:  Fri, May 15, 2015 05:51 PM
> To:  "ome-users"<ome-users at lists.openmicroscopy.org.uk>;
> Subject:  ome-users Digest, Vol 122, Issue 17
> 
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> Today's Topics:
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>    1. Re: Error to Open .czi File (William Moore)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 15 May 2015 10:51:23 +0100
> From: William Moore <will at lifesci.dundee.ac.uk>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Error to Open .czi File
> Message-ID:
> <5A6720B2-23AB-4433-B56E-A7E3014CDC1E at lifesci.dundee.ac.uk>
> Content-Type: text/plain; charset="windows-1252"
> 
> 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.
> 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>_______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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