Opening 2D Tif files larger than 2 gigapixels

Hi,
has anyone experience with opening a 2D image file with size ~66K x 66K? I have one generated by stitching multiple fields of view on a Leica widefield, and exporting the result in Tif format. I tried with ImageJ and few others, without success. So far I only managed to open subsets of it, no larger that 2 gigapixels, in ImageJ.
Thanks in advance,
Giovanni

@gcardone,

Short answer - it’s very hard to do that (maybe impossible) with “vanilla” ImageJ [1].

It is possible to view images of that size by being clever - e.g. we routinely do it using BigDataViewer (“bdv”) (though in our case its usually huge 3d volumes). If you can convert your 2d image to a format that bdv likes, e.g. hdf5. Let me know if you want to try that, I (or others) can try to help you.

Since you’re doing stitching, I suggest you check out BigStitcher (its uses bdv).

John

[1] Because arrays in java are limited to ~2.1 billion entries

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HI @gcardone,

@bogovicj already mentioned the 2GB Java limit which is why very large planes cannot be opened at once in a traditional ImageJ viewer. Independently of the language limitations, the general approach when dealing with very large images (across XY but also Z) is to build downsampled copies of the original images at multiple resolution levels and store them in a capable format

There are several open format solutions that have support for multi-resolutions including the BigDataViewer HDF format, the Imaris IMS format or more recently the OME-TIFF format.

On top of this, there are also mutiple software solutions to read and display multi-resolution image formats. In ImageJ, @bogovicj mentioned BigDataViewer which is the reference plugin for handling multi-resolutions images. Outside the ImageJ ecosystem, QuPath is an alternative. If you are managing data via OMERO, OMERO.iviewer also has support for multi-resolution images.

Best,
Sebastien

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