⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 1236 - Unable to display big images (~10 GB)
Unable to display big images (~10 GB)
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-03-02 09:04 CST by gherardo
Modified: 2016-04-26 16:47 CDT
3 users (show)

See Also:
Description gherardo 2016-03-02 09:04:57 CST 
I am using the new version of FIJI with JAVA 8 on Ubuntu 14.04 
When I open a big image (like 4GB, 10 GB) the window that opens appear gray, like with no image rendered over. The image is actually loaded but I am unable to see it, if i place the cursor over the image it shows the pixel value in the fiji bar and all the plugin that acess image pixels work normally.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.16.0-60-generic
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b17
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b17
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/cig-gherardo/ownCloud/Segmentation/Fiji.app/java/linux-amd64/jdk1.8.0_66//jre
  imagej.dir => /home/cig-gherardo/ownCloud/Segmentation/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160217160804)
Fiji: http://update.fiji.sc/ (last check:20160218145537)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160226213340)

Files not up-to-date:
  a3c533dc (LOCAL_ONLY) 20160229151649 macros/toolsets/PSDtoolset.ijm
  74fcdc3a (LOCAL_ONLY) 20160222160632 plugins/Map_tool-0.0.1-SNAPSHOT.jar
  673adfd6 (LOCAL_ONLY) 20160219154426 plugins/Multiscale_Mexican_Hat-0.0.1-SNAPSHOT.jar
  318dae2a (LOCAL_ONLY) 20160222102936 plugins/StackJoin_-0.0.1-SNAPSHOT.jar
  16dfb333 (LOCAL_ONLY) 20160229130618 plugins/_ObjCounter-0.0.1-SNAPSHOT.jar
Comment 1 Mark Hiner 2016-03-02 09:46:12 CST 
What is the bit type of your image? Since the pixel values are there, is it possible that image display range just needs to be updated?

See:
http://imagej.net/Troubleshooting#The_image_I_loaded_is_displayed_all_black.21_But_it_is_not_black.21

Hopefully it's just a matter of adjusting Brightness/Contrast!
Comment 2 gherardo 2016-03-03 02:24:36 CST 
It is a 8 bit stack of image (15 slices, 43008x21504 pixels).
No the problem is not a matter of contrast, I tried but it's not working. Moreover is not that I am looking a dark image, but no image at all, the image window is totally gray (like the background of the window frame of the GUI). I am just trying to guessing now but it is not possible that is a problem of rendering capabilities? like somehow the graphics can't render so many pixels.
The problem persist if I just take one of the slide (43008x21504 pixels, 882 MB). I tried to scale the image and if it is scaled to 10752x5376 pixels (174 of the original) the image appear correctly. 
I remember that prior to the upgrading to Java 8 images of around 1 Gb were showing correctly. I tryed to download the Fiji Life-Line version, 2014 November 25 but I have the same behaviour.
Could be I messed up with something and FIJI is not using properly the graphics?
How can I have a fresh installation in Ubuntu (it is not sufficient to download it and extract it?).
Thanks.
Comment 3 Curtis Rueden 2016-04-26 16:47:38 CDT 
> the image window is totally gray (like the background of the window
> frame of the GUI). I am just trying to guessing now but it is
> not possible that is a problem of rendering capabilities? like
> somehow the graphics can't render so many pixels.
  
That does seem like the likely issue, yeah.

> How can I have a fresh installation in Ubuntu (it is not sufficient to
> download it and extract it?).

What do you mean by "not sufficient"? As in: you download and extract
it, and the problem still occurs?

You can try the Edit > Options > Reset... to fully reset the ImageJ
settings.