[ome-users] Analyzing extremely large images from AxioScan/ZEN software

[Balaji Ramalingam]

Hi,

Memory management is very important in such cases, and there are multiple ways to handle these files.

The documentation for the same is given in here,
http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/managing-memory.html

Please try the suggestions in here and let us know if the issue persists.

Best,
Balaji



__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Trevor Steve <tsteve at ualberta.ca<mailto:tsteve at ualberta.ca>>
Date: Tuesday, 9 September 2014 17:51
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: [ome-users] Analyzing extremely large images from AxioScan/ZEN software

Hi All,

I am attempting to analyze extremely large images produced on an AxioScan microscope and segmented using ZEN software.  These are CZI files with JPEG-XR compression.

Examples of my image sizes (pixels) are:
201276 X 203751
205353 X 198345
182611 X 215607
167046 X 189615
135139 X 188422
158073 X 165835
185008 X 144463

When I run the .CZI to .TIF converter http://hcbi.fas.harvard.edu/resources_software
I end up with TIF files which are, as an example:
182612 x 215608 (> 39 GPIX), 74.3-80.2 GB

These massive TIFF files cannot be opened by ImageJ (Bio-formats), Fiji, or Photoshop (CS5).

I am wondering if anyone has found a solution to working with this type of data.  Is it possible to reduce the resolution/size of the images produced by the microscope/ZEN software?

Thanks,

Trevor



--
Trevor Steve, MD

Neurology Resident (PGY-7)
PhD Student, Department of Medicine
University of Alberta

The University of Dundee is a registered Scottish Charity, No: SC015096
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