Open Microscopy Environment

Hi,

The FAQ section at http://www.openmicroscopy.org/site/support/faq contains the question "Does Omero store data in OME-TIFF/OME-XML format?" which I was wondering about, though the answer is not as specific as I wished.

What remains unclear to me is what happens if I upload a 32-bit float image to the Omero server and export it later on. Will the image remain 32-bit float with unchanged voxel values? From testing this myself I understand that the image will indeed remain unchanged, but I cannot know whether this will always be the case.

Moreover, the answer at the FAQ section states that the image "binary data is stored in a optimized proprietary format in the Omero binary repository". Does anyone know what kind of format that is?

I'm concerned about loses in my files while importing/exporting but couldn't figure out from the documentation what Omero does in this regard.

Thanks a lot for any help!

Hi,

The Pixel data are stored without changing the values in any way, so you should never lose or change any pixel values. The binary storage format is basically the pixel values alone, with no header etc. All the dimensions, metadata etc are stored in the database and used to access the correct pixel values for rendering planes, exporting the data etc.

One option you have if you have particular concerns about losing any data, or you want to be able to retrieve the imported file in it's original format, is to archive the original file that you import (look for this option during import). Then you will be able to download this file. However, this does mean that you double the disk space usage for each image you import.

Hope that helps,

Hi wmoore,

Thanks for your answer, it does help. One more question though. I understand now that importing files into Omero does not affect the dynamic range of the images. The same holds for downloading data from Omero, as the downloading option implies original formats. But, what about exporting to Ome-tiff?

The option of exporting to Ome-tiff would be enough for me but I can't find a statement in the Omero documentation where I can read about the dynamic range of these Ome-tiffs. Are the exported Ome-tiffs always 32-bit images?

Thanks again!

The Pixel type of the exported images will be the same as the imported ones (same as the Pixel data in the OMERO binary repository). So, int8 will be int8, float (32) will be float etc.

The OMERO database supports these pixel types, which correspond to similar values in OME-TIFF.

Code: Select all

# select * from pixelstype;
id | bitsize | permissions |     value      | external_id
----+---------+-------------+----------------+-------------
  1 |       1 |         -35 | bit            |           
  2 |       8 |         -35 | int8           |           
  5 |       8 |         -35 | uint8          |           
  3 |      16 |         -35 | int16          |           
  4 |      32 |         -35 | int32          |           
  6 |      32 |         -35 | uint16         |           
  7 |      32 |         -35 | uint32         |           
  8 |      32 |         -35 | float          |           
  9 |      64 |         -35 | double         |           
10 |      64 |         -35 | complex        |           
11 |     128 |         -35 | double-complex |