Open Microscopy Environment

BACKSTORY: I'm trying to save ~10GB of imaging data into a tif file from Fiji using the Bio-Formats Exporter and I can't get any of the (non-OME) Tif formats (.tif, .tiff, .tf2, .tf8, .btf) to save the dimensionality data (Channels, Times and Zs). OME-TIFF does, but even after 5.1.1 this format still doesn't seem to be able to save files >4GB.

You can recreate this by creating a new hyperstack (2 channels, 5 frames), then exporting as any of the tif formats (I used uncompressed). Importing these back into Fiji (using the Bio-Formats Importer) opens them as a single sequence (of 10 timepoints).

The OME-XML looks like this:

<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="1" SizeT="10" SizeX="512" SizeY="512" SizeZ="1" Type="uint8">

Is there something simple that I'm missing to save (big) files with dimensionality data using the bioformats exporter? Unexpectedly, the basic Fiji SaveAs (specifying Tif) does save the dimensions.

Any thoughts appreciated,

Dave

Hi Dave,

This is expected behavior - plain TIFF files have no mechanism for recording the dimensions.

Support for >4 GB OME-TIFF export in Fiji will be present in the upcoming 5.1.2 release; specifying the .ome.tf2, .ome.tf8, or .ome.btf extension will enable this automatically.

-Melissa

Hi Melissa,

Thanks for the clarification. I'm very pleased to hear that the 4GB+ versions of OME-TIF are coming.

Best,

Dave