Open Microscopy Environment

Hi all,

A new magical problem most likely specific to VSI and hot Olympus saves their data has come up recently.

We were testing different compression formats available to the VSI container and found something.

When saving images acquired with an RGB camera with 'No Compression' on the software, we find that the channel order is different when opening it using Bioformats.

It appears that they are opened ad B->G->R and not R->G->B, which lead to a lot of strange confusion, seeing as most formats when saving multichannel images from RGB cameras use the order R->G->B. And when the white balance is well made on the images, it is hard to notice that there is a problem, depending on the stainings.

I've added a dataset which contains a jpeg-compressed example (Opens as RGB as per the jpeg standard) and the uncompressed dataset, which opens as BGR.
http://qa.openmicroscopy.org.uk/qa/feedback/17694/

Again I am not saying that this is a problem with BioFormats but I would appreciate help with the following points.

1. How can I find out using BioFormats Macro Extensions, what kind of compression was used on the dataset?
2. Ideally, would there be a way for Bioformats to understand this particularity and adjust the LUTs accordingly?

Thank you very much for your time!

Oli

Hi Oli,

Firstly thank you gain for the uploaded sample files as they are very useful for debugging and further developing the readers.

I was able to do some initial debugging on the files you provided and I can see the effect you mentioned with regards the channel orders. For the 2 files provided Bio-Formats recognises the compressed file as being of type JPEG and the uncompressed file as being type RAW. Unfortunately there is not currently a macro extension to retrieve these values.

With regards the second question, we would absolutely like to be able to resolve this and update the reader, in order to do this we would need to know if this behaviour was consistent for all uncompressed files or if there was any existing metadata or tags within the file that would allow Bio-Formats to recognise the ordering.

David Gault