Open Microscopy Environment

I work with scanning / transmission electron microscopes (STEM and TEM), and FEI is a large company that makes these microscopes. Their TIA (aka ESVision) software saves data in a proprietary .EMI format and an open .SER format. It would be extremely useful to add .SER format import to bio-formats as many microscopists would benefit from this.

I wrote fully functioning .SER readers in both python and matlab. I do not have time (or the experience) to transfer this to a bio-formats C++ reader. I will happily share example data files (images and image stacks) and the readers if someone can port the code.

Thank you for offering to send sample data and code. We would certainly be interested in adding support for .ser files to Bio-Formats (though please note that it is written in Java and not C++).

The easiest way to send files to us is by uploading a Zip file to:

http://qa.openmicroscopy.org.uk/qa/upload/

If that doesn't work, or you are sending a file larger than 2 GB, please let me know and I will send alternate instructions.

Thank you for the reply. I will package up some images and the python code. Thanks for the clarification about java. I hope this functionality can be implemented because it would be very useful to many electron microscopists.

Thank you for sending example data and code. There is now a ticket for this on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/12057

If you would like to be automatically notified of updates to that ticket, please let me know and I will make sure that you are CC'd.

I would like to second the demand of Percius. We are an EM lab - mainly single particle TEM. We also work with FEI microscopes and produce EMI/SER images regularly. To keep the metadata of the images it would be helpful to be able to import them to OMERO.
Best regards,
Gabor

Hi Gabor,

thanks for your feedback. Given the large numbers of requests for new format readers, it is certainly helpful for us to have a sense of the community needs in order to prioritize the Bio-Formats work. If you are interested, we can cc you on the Trac ticket.

Best,
Sebastien

Hi, I would also be REALLY interested by having a .ser file reader, because my lab has many different FEI microscopes. I read on the site that the .ser reader was originally scheduled for version 5.1, but it was finally modify to 5.X.
Any precision?

Hi,

as we explained in our most recent blog post, the work for Bio-Formats 5.2.x is primarily aimed at upgrading our Data Model to improve the ROI usability.

This implies we will not be adding any ​more readers (other than those currently scheduled) to Bio-Formats 5.2.0 and the ticket you are mentioning was rescheduled for 5.x. If anyone has the expertise to help with the development of this reader, we welcome your input via GitHub - some docs are available to write new format readers and contributing to Bio-Formats

Best,
Sebastien