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

[Trevor Steve]

Hi Balaji,

Thanks for your suggestions.

To clarify my problem, we are dealing with *single images* with 182612 x
215608 pixels (~ 40 GPIX).  As we are not dealing with a stack of images,
as far as I am aware "extremely large image planes are not yet cached in
ImageJ tilewise"

>From what I have heard, "this is a future goal of the project"

* https://github.com/scifio/scifio/issues/125
* https://github.com/imagej/imagej/issues/87

With respect to the work-around of cropping on import....as far as I
understand, the current ImageJ plane limitation of 46340 x 46340 pixels (~2
GPIX) would require us to crop our image (182612 x 215608 pixels) (~40
GPIX) to approximately one twentieth its original size, which is obviously
unacceptable.  I suppose theoretically one could perform this operation
twenty times, and if you were able to reconstruct the resulting image, this
would be useful.  However, this is well beyond my area of expertise. If
anyone has a potential solution, it would be much appreciated.

Trevor


On Wed, Sep 10, 2014 at 1:36 PM, Balaji Ramalingam <
b.ramalingam at dundee.ac.uk> wrote:

>  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>
> Date: Tuesday, 9 September 2014 17:51
> To: "ome-users at lists.openmicroscopy.org.uk" <
> 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
>



-- 
Trevor Steve, MD

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