Open Microscopy Environment

Hello OME Team,

I tried using the IRC to ask a quick question but I think the browser kicked me out of the session so apologies if there were replies there.

We've recently had an Andor Dragonfly installed at the Liverpool CCI and we're getting all sorts of interesting multidimensional data that mostly open OK with BioFormats (there are some java console errors thrown).

Please let me know if you would like some datasets for Bioformats QA and if so, are there any specific modalities that would helpful (multipoint, tilescans, looped protocol acquisitions, all of the above). I'm happy to make a mix. I seem to remember last time I checked the format spec that you don't have many IMS v3. Fusion can save these out so I can always double-down and save as both.

Please let me know if this would be helpful,

Best,

Dave

Hi Dave,

Thanks for getting in touch, more sample data is always very much appreciated. We do have a specification document and some sample datasets for 5.5, we have much less data on the older IMS 3 tif based format. If there are specific files that you are seeing missing metadata or java errors in the console then those would certainly be good to have, otherwise a selection of different modalities would be good to add to our test suite.

Any files you can upload to https://www.openmicroscopy.org/qa2/qa/upload/
Also would it possible to make any files provided public and published under a CC-BY license (http://downloads.openmicroscopy.org/images/)?

Thanks for the reply, I've just uploaded a bunch of files through QA.

The names should be fairly self explanatory, but there are multichannel, multislice and multitime files (and combinations) with some post-processing (done in Fusion) for both stitching and deconvolution. There is also some SRRF processed data: a single slice and a z-stack.

Imaris writes out a metadata text file with the images so I've included that too.

Convallaria_3C_10T_confocal.ims
Convallaria_3C_10T_confocal.txt
Convallaria_3C_1T_2x2grid_confocal.ims
Convallaria_3C_1T_confocal.ims
Convallaria_3C_1T_confocal.txt
Convallaria_3C_3T_2x2grid_confocal.ims
Convallaria_3C_3T_35Z_confocal.ims
Convallaria_3C_3T_35Z_confocal.txt
Convallaria_3C_3T_35Z_confocal_deconvolved.ims
Convallaria_3C_3T_35Z_confocal_deconvolved.txt
TransFactors_2C_34Z_SRRF.ims
TransFactors_2C_34Z_SRRF.txt
TransFactors_2C_SRRF.ims
TransFactors_2C_SRRF.txt

I was mistaken before that you cannot save files as IMS v3 in Fusion but I've resaved the same files in Imaris (v9.2.1). Hopefully that's of some help (the files are suffixed with "_IMS3").

I'm happy for these to be added to the repository as CC0, I don't see any need to restrict them further.

Best,

Dave

PS. the images are really boring (IE timelapses of fixed samples) but I assume that's not a problem for formats testing!

PPS. I just realised that I got the names wrong and there are only 17 (IMS5) or 15 (IMS3) slices for the SRRF stacks not 34 as labelled. Let me know if you need more details.

Thats brilliant Dave, thank you for taking the time to put those together. We received all of the files just fine, I will get them tested and configured in the next day or so and then we will include them as part of our data repo which we run automated tests on every day.