Posted by
ctrueden on
Jan 15, 2016; 10:47am
URL: http://imagej.273.s1.nabble.com/Large-image-tp5015380p5015389.html
Hi Sho,
> What is the largest size image FIJI can open? By that I mean, the
> biggest number of pixels in x and y (and I guess z, though not
> relevant at the moment).
As Wayne says, there is a 2 gigapixel limit when opening and displaying
image planes using the ImageJ (1.x) user interface's default image viewer.
> Is there any way to circumvent this limit?
One major goal of the ImageJ2 project is to break this limit.
ImageJ2 uses the ImgLib2 library [1] as its data model, which has much
larger limits on the number of pixels (theoretically: ~2^63 per dimension,
up to ~2^31 dimensions, totaling ~2^63^31 pixels).
Hence, you can open larger images using the ImageJ2 API. But you will not
be able to display them in the user interface yet.
The SCIFIO library [2] also supports opening such images on-demand, so that
blocks are read from disk as you iterate over the image. This is similar to
(but more powerful than) ImageJ 1.x's virtual stacks feature.
In this way, you can write code to process these large images without
displaying them.
The Fiji project [3] already includes the BigDataViewer (BDV) plugin [4],
which currently functions as an alternative viewer, to display arbitrarily
large images backed by ImgLib2. In the future we hope to integrate
BDV-driven UI technology more completely into ImageJ core. But there are a
couple of limitations right now:
1) BDV was originally designed for large SPIM data; opening large image
files more generally currently requires some coding. But we want to change
this.
2) Many ImageJ 1.x plugins assume the data is stored in an ImageJ 1.x data
structure, which is not what BDV uses. So "mixing and matching" IJ1 and IJ2
functionality is tricky here.
But we are working to lift these restrictions as time goes on.
Regards,
Curtis Rueden, ImageJ2 architect
Tobias Pietzsch, BigDataViewer architect
[1]
http://imagej.net/ImgLib2[2]
http://imagej.net/SCIFIO[3]
http://imagej.net/Fiji[4]
http://imagej.net/BigDataViewerOn Thu, Jan 14, 2016 at 3:01 PM, Sho Fujisawa <
[hidden email]> wrote:
> What is the largest size image FIJI can open? By that I mean, the biggest
> number of pixels in x and y (and I guess z, though not relevant at the
> moment). Is there any way to circumvent this limit?
>
>
> Sho Fujisawa
> Sr. Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E. 68th St.
> Zuckerman Room 1834
> New York NY 10065
> (212) 639-6667
> (646) 888-2186
>
>
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