Image Reader fails with large image planes

[imagejan]

When trying to read images with more than ~20000x20000 pixels (czi files > 4GB), Image Reader fails with:

Encountered exception while reading image 1-2-Scene-2-ScanRegion1.czi! Caught Exception: Array size too large: 3 x 26082 x 26082 x 2

Switching to Cell Image Factory in the advanced options leads to:

Encountered exception while reading image 1-2-Scene-2-ScanRegion1.czi! Caught Exception: No compatible service: io.scif.SCIFIOService

As a workaround, it would already help to have a crop option for import, see #317.

[dietzc]

Thanks @imagejan! I will take a look.

[beschu]

A sample .czi file of this size would be very useful, as it is hard to get access to such images.

[tibuch]

@imagejan can you send us a .czi file for testing?

[imagejan]

@tibuch @beschu I can't share the file publicly, but I can upload it somewhere for you to access. Do you have a KNIME ftp server for these cases? The file is about 4.5 GB.

[imagejan]

I uploaded an example file (1-2-Scene-2-ScanRegion1.czi) to the ftp server as communicated by @gab1one. Thanks for looking into this.

[maierl]

ah, sorry for the duplicate :)
just as a wrap-up: this bug also affects TIFF files read by the latest stable version of KNIP shipped with KNIME 3.3.1.

[imagejan]

Our users (neurobiologists working with large stitched z-stacks) repeatedly keep running into this issue, so here's a small update:

The Image Reader also fails on ics/ids files that are >4GB in size in total, even if the single planes are much smaller than 4 Gigapixel. It think it is related, or should I open a new issue for this one?

[dietzc]

@imagejan can you share the file with me somehow?

[imagejan]

I'll upload a sample ics/ids dataset later today to the same ftp server as discussed above, alright?

[imagejan]

I uploaded the 4.6 GB dataset consisting of mosaic_1.ics and mosaic_1.ids into the incoming root folder of the ftp server.