Open Microscopy Environment

Hi all,

Just started working with a SPIM scope that writes each stack in a separate tiff file. Was wondering if it would be possible to have bioformats recognise the format and read all the stacks as one big movie.
Have uploaded a dataset for you guys with ID 7540.

Cheers,
Helio

Hello Helio,

Thanks for the dataset.

Can you answer a few questions about what it came from:

What is the make and model of the scope?
What application (vendor, name, version, website) was used to save the files?

When I get this information I can make a ticket for the work.

I have had a quick looks at some of the individual TIFF files.
They all seem to be totally black, is this expected?

Ta,

Andrew

Hi Andrew,

The microscope is a mDigital Scanning Lightsheet microscope. Its an in-house built by EMBL-Heidelberg and to be honest I don't think they have a website.
I will try and find out the version of the software that created the files.

I realize that this is a very much niche file format so would understand if you guys can't really do much about it.

About the files they should not be black. They in principle are 16bit files with some sort of fluorescence. Maybe it was the compression. Let me know if you need and I can upload the original files.

Cheers,
Helio

Hello Helio,

Thanks, I have made a ticket on trac:

https://trac.openmicroscopy.org.uk/ome/ticket/11318

Ta,

Andrew