Open Microscopy Environment

Hello everyone,

I'm posting here an issue about the usage of Omero with really specific format.
In my lab we are using a lot of Gatan Digital Micrograph Format (DM4/DM3). When using Omero option "right click > open with", we are able to open it with Gatan Digital Micrograph. However, Omero does not send the orginal DM4/DM3 file but a TIFF filethat loss many of the metadata like calibration. To do so we are obliged to manually download the file, and then work on it which is quite inconvenient when we work in a large set of data. We would like to know if there's a way "open with"' links the original file and not the converted one.

Thanks in advance.

Dear Victor

From your post, I assume you are talking about opening File using the OMERO plugin,OMERO.insight-ij, for ImageJ.
In older version of the plugin, we used to open the file as OME-TIFF. In most recent versions, we use Bio-Formats to read the file in its original format.
Could you indicate the version you are using?

Thanks

Jean-marie

Jean-Marie,

Thanks for your kind answer. In fact i'm not talking about the image J plug-in but the open with function in omero insights. To be clearer, here is an example :

1- I upload a "dm4" file like "example.dm4" in omero in a given project/library.
2- Later on, i wanna work on the given file with the appropriate editor like "Digital Micrograph".
3- Therefore, i right click on the file inside OMERO insight and select "Open with" and then click on the desired editor. Then, "activites" pannel pop.up and open the file with the editor.

But ! Here is the problem : it's not the original "example.dm4" that has been sent to the editor but "example.dm4.ome.tiff". Thus, all the orignal metadata in the ".dm4" file is not available inside the editor.

The only option available is therefore to do the "right click -> download" to obtain the original "example.dm4" and then use the propper editor and it's a long operation for big data sets. Therefore, i was asking if there was a possibility, even by modifying the source code, to make the "open with" function in OMERO insight to link the original file and not a generated TIFF.

Hi Victor

Thanks for the detailed information
Using OME-TIFF in the "open with" option was introduced at the time when we did not always have accessed to the original image (pre-FS). For more recent installations of OMERO, this is not necessary to have that approach.
Your suggestion makes sense and it will be useful to have.

I have opened a Pull Request [1] allowing to download the original image or an ome-tiff by setting a value in the configuration file (container.xml)

Hopefully it will be included in the next release

Cheers
Jmarie

[1] https://github.com/openmicroscopy/openm ... /pull/5793

Hi Jean-Marie,

Thanks for taking account of my post and proposing such changes. We're impatiently waiting for next release.

Best regards,
Victor