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

[Melissa Linkert]

Hi Trevor,

> 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"

All completely understood.

> 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.

The only ImageJ plugin I know of that might be able to open the entire image
is the VSI Reader ActionBar plugin from EPFL:

http://biop.epfl.ch/INFO_completed_projects.html

It was not designed for the file format that you are using, but it was designed
for very large whole slide images (and uses Bio-Formats internally, so
in theory could still open your files).  I have no experience with using
that plugin, though, and you would need to contact BIOP EPFL for
support.

If that plugin doesn't work, then yes, you will need to open the image
as ~20 separate tiles.  This can be done in a macro - selecting
"Plugins > Macros > Record..." and then opening a tile will show you
what the corresponding macro code should be.  Provided that you keep
track of which open image window corresponds to which (x, y) coordinate
in the original image, reconstructing the image should be
straightforward.  Further information on writing macros is available on
the ImageJ website:

http://rsb.info.nih.gov/ij/developer/index.html

Regards,
-Melissa

On Wed, Sep 10, 2014 at 04:24:20PM -0600, Trevor Steve wrote:
> 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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