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

Sun May 17 13:33:29 BST 2015

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

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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:

   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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