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HI Anthony,

I am assistant director at Experimental Pathology (ExpPath) at NYU Langone Medical Center, we deployed OMERO Plus (the commercial distribution of OMERO) on 2019 specifically for image data management.

Specifically on usage: We have been pretty successful on the adoption side because the only way researchers could access image data produced at our research lab was by requesting OMERO access. ExpPath produces image data for a lot of researchers (~200 labs) and therefore theres a lot of use. On other models of OMERO deployment it is up to each researcher to import/upload their images to OMERO, we have that option available but it seems that data coming in through that route is limited to a handful of researchers.

Regarding Data Management overall: OMERO as you rightly point out is an image data management platform and is not intended to work with other data so as an overall solution it is not appropriate.

Regarding asking an individual core lab to set up and manage OMERO is tough. At NYULMC OMERO Plus is a joint effort between ExpPath and the Medical Center's  Information Technology department, without IT resources it would have been impossible for us as a single core lab to set it up. Management of user access relies on a combination of efforts from IT and us for which we have developed workflows but it's taken 50% of my time even with all the IT support. 

I hope this helps a little, please do reach out if you want  to discuss further.

Best regards,

Valeria Mezzano

NYU G. Sch. of Medicine

Experimental Pathology [RRID:SCR_017928]

Hi,

I am deeply involved in many imaging data/metadata management projects (Canada Bio-Imaging, BioImaging North America, Global BioImaging, quarep.org, Montreal Neuro Open Science Institute, etc).  All wanting to achieve open, reproducible and F.A.I.R. science. I would like to share a few things.  First, remember that OMERO uses the Bio-Formats library, hence it reads ~160 different file formats.  Also, for imaging data, data  visualization is essential, unlike other science modalities (eg. genomics, flow cytometry etc).  OMERO allows you to peruse multi-dimentional datasets very efficiently, without having to first download them.

Yes OMERO has a learning curve however, there is so much materials around now to assist people in getting started!  Once your users start using OMERO.figure to prepare the papers, power point etc, I guaranty they will never use anything else.  It is true however that installing/running an OMERO server requires Linux IT skills.  For that reason, it is probably easier to go for institutional, or national initiatives.  In Canada, we are lucky to have an OMERO instance running in the cloud infrastructure of the Digital Research Alliance of Canada.  It's been running with minimal efforts for a few years now.  We are also using it to document the quantitative performance of microscopy equipment as per ISO 21073.

As for the Interoperability of scientific data, you should know that RENCI iRODS is working on connecting to OMERO.  Also, I want to remind here that OMERO does a lot more that data management.  First, there is a Fiji plugin to work on images stored in an OMERO instance.  Secondly, there are a number of scripts for data processing and analysis coming with an OMERO installation.  It is also possible to upload scripts to execute data processing/analysis within OMERO.  Lastly, if you are working with large datasets and/or complex workflows, one can run virtual environments (e.g. Jupyter) and work on data contained in OMERO.

Hope this is useful!  Remember that BINA, GBI and QUAREP have regular gatherings on the subject of data management.  Everybody is welcome to join this world community!  We all share similar challenges with data management.

Best regards,

Judith

Hi Anthony!

I use OMERO at the University of Nebraska Medical Center for data management for multiple cores. Right now we use OMERO as a way to quickly get data from whole slide scanners to researchers. Every person who uses our lab has an OMERO account and know that is how they will get their data. Hope that helps!