• The University of Arizona instance of OMERO is funded from the U of A Health Sciences strategic plan, initiative 5.3 “Health Analytics Powerhouse”.
• Oversight for the OMERO project comes from the Data Science Institute and broadly fits in within the Soteria project. Nirav Merchant is the director of the DSI, Rudy Salcido is the project manager for the UAHS 5.3/Soteria initiative, and my role is to move OMERO forward. Of note, my role supporting OMERO is not full time, I wear several other ”hats” that have expectations for my time as well.
• Soteria is a secure network environment designed to work with HIPPA/PII type data. OMERO is not “inside” Soteria, so all data stored in OMERO must be de-identified.  Research projects using OMERO do not need to use Soteria, but it’s there in case people have data that needs to connect to clinical information.
• Our first OMERO pilot project came from the interests of Dr. Curiel, who is developing an image database of skin lesions that they have named PRIT. The patient skin lesion image data stored in OMERO is de-identified, but it is cleverly linked to clinical data (RedCap) and biospecimen data (OpenSpecimen) using unique identifiers. We worked with skilled personnel from the University’s Center for Biomedical Informatics & Biostatistics (CB2) to pull all these pieces together in a coherent manner.
• Our second OMERO pilot (Dr. Zavros and colleagues) is planning to combine spatial transcriptomics with multiplexed fluorescence imaging of tissue sections to create atlases of two different types of cancers. This project will also coordinate with data in RedCap and OpenSpecimen.
• Pilot projects do not need to have clinical components. There's room and support for labs that use a number of different imaging modalities and just need to keep their data organized.
• The OMERO workshop was intended not only for training, but also to allow labs to see what was possible and hopefully encourage them to “get on board”. Since this project was internally funded, it’s important to show those who approved the funding that OMERO is being used and is of value to the research community.

• The University of Arizona instance of OMERO resides on server housed in the UITS building on Mountain & Speedway.
• The U of A OMERO server has 100TB of space apportioned to it. I have told people this won’t be enough space, but we can work on getting more once we can demonstrate that we are on a trajectory to run out of file space.
• Access to the U of A instance of OMERO requires the use of the campus' Virtual Private Network (VPN). This has pros and cons.
  • PRO – adds an extra layer of security. OMERO does not yet work with the Shibboleth single sign-on (OME is working on it, since Shibboleth is used at many other institutions). Since access to the U of A VPN requires a valid UA NetID, it is a way to ensure that if someone leaves the U of A, they cannot easily get access to lab data stored on OMERO.
  • CON – the VPN makes sharing with off-campus users a bit more challenging. Off-campus users would need to become designated campus colleagues (DCC).
• As we saw in the workshop, OMERO can be accessed using OMERO.insight (the desktop client, required for user-friendly uploading of data using the desktop GUI), OMERO.web (using a modern web browser), or the command line interface, OMERO.cli (for those who need routine procedures to be run via a Python script). Regardless of how you access the University’s OMERO server, you will still need to be on the U of A VPN to get that access. We recommend using: vpn.arizona.edu/full
• The University of Arizona OMERO server was updated (Nov 2023) to the latest server version, which includes all the plugin functionality that was demonstrated at the workshop (iviewer, figure, fpbioimage, parade)
• Also available (on a different server) is the U of A’s instance of XNAT (general info, University of Arizona info), which is open-source software for working with medical imaging type data (MRI, CT, ultrasound, etc), primarily in the DICOM file format. The XNAT team is also looking for pilot projects.

Image

• There is more to working with OMERO than putting images on a server. Based on my experience in microscopy core facilities, some labs have a strong understanding of what’s involved with data management and others will need some time to get up to speed. See the data lifecycle graphic here and the reading list below for more resources.
• We strongly urge you to start with a small, manageable project. Coming up with a plan for organizing your data, developing standardized text describing husbandry/culture conditions, experiments, sample prep techniques, as well as ensuring that you have procedures for getting the data (and deciding what data) into OMERO, post-processing techniques, image analysis, and so on will take some time. Starting small and then adding in additional projects once you have worked out the details will ensure that moving to OMERO doesn’t slow down your entire lab.
• We have a template that we will share with you for proposing an OMERO pilot project (3-6 months, depending on the scope of the project). The pilot document helps us understand what you want to accomplish and then helps keep the entire project on-task.
• As a reminder, all clinically-related data on OMERO must be de-identified.
• We will also be looking for feedback from you (lessons learned) as we go along. This way our team can continue to get better at helping others move into using OMERO.
• We will also need faculty members to serve on our governance committee. We need help to develop parameters to ensure that this resource is used responsibly and equitably, as well as to advocate for continued support from the University of Arizona’s research administration.

There’s a lot of work being done around the world to come up with organized methodologies and structures to ensure that image data management is done well (much of it is still a work-in-progress). Here’s a short list of recommended reading:

• Briney KA, Coates H, Goben A (2020) Foundational Practices of Research Data Management. Research Ideas and Outcomes 6: e56508. https://doi.org/10.3897/rio.6.e56508
• Michener WK (2015) Ten Simple Rules for Creating a Good Data Management Plan. PLoS Comput Biol 11(10): e1004525. https://doi.org/10.1371/journal.pcbi.1004525
• Guillermo Marqués, Thomas Pengo, Mark A Sanders (2020) Science Forum: Imaging methods are vastly underreported in biomedical research eLife 9:e55133  https://doi.org/10.7554/eLife.55133
• John M. Heddleston, Jesse S. Aaron, Satya Khuon, Teng-Leong Chew; A guide to accurate reporting in digital image acquisition – can anyone replicate your microscopy data?. J Cell Sci 15 March 2021; 134 (6): jcs254144. doi: https://doi.org/10.1242/jcs.254144
• Reporting and reproducibility in microscopy, Nature Methods 18, Dec 2021 - https://www.nature.com/collections/djiciihhjh (multiple articles)
• ELIXIR Research Data Management Kit - Bioimaging data - https://rdmkit.elixir-europe.org/bioimaging_data
• Nelson, G, Boehm, U, Bagley, S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021; 284: 56– 73. https://doi.org/10.1111/jmi.13041

FASEB has a data management initiative - https://www.faseb.org/data-management-and-sharing

• NIH Feedback One Year After Implementation of the DMS Policy (FASEB blog post, May 2024)

The Univeristy of Arizona Library has a Data Cooperative team (https://data.library.arizona.edu/). The team’s website provides helpful information about data management, occasional workshops, and people to help with questions regarding structuring your data for future sharing, as well as assistance with data visualization and Rstudio.

We have developed some materials to assist interested University of Arizona users in getting started.

• Accessing OMERO at the University of Arizona - (PDF, 5/2024, D. Cromey) - setting up the U of A VPN, installing and configuring the OMERO.insight desktop client (Windows, MacOS, Linux).
• Organizing & sharing data: Groups & Users in OMERO - (PDF, 5/2024, D. Cromey) - in revision
• Relevant resources from the Open Microscopy Environment team:
  • Managing an OMERO Group - (PDF, OME team) helpful document for users with the Group Owner role.
  • OMERO walkthrough for facility managers - (Online wiki, OME Team) 
  • Data Management and Cooperation - (Online Wiki, OME team) - 
  • Managing Data - (PDF, OME team) - 
• We have the recordings from the Aug 2023 on-site training workshop on D2L (https://d2l.arizona.edu/). Email us to request access. (NOTE: the D2L site is only available to users with UA NetID logins)

OMERO resources from the Open Microscopy Environment (and the open-source community):

• Support - https://www.openmicroscopy.org/support/
• Documentation - https://omero-guides.readthedocs.io/en/latest/
• https://forum.image.sc/ is an online community support website for OMERO, ImageJ, CellProfiler, QuPath, and many more open source software tools.
• The presentations from our workshop - https://downloads.openmicroscopy.org/presentations/2023/Arizona/
• Play with OMERO using the OME demo server - https://www.openmicroscopy.org/explore/
• WORKSHOP TIP: if you are reading the OMERO documentation/help documents, look at the URL in your web browser. If the URL has a specific version number, select that number in the address bar of your browser (between the / characters) and replace the number with the word “latest” to ensure you are reading the most up-to-date version of the documentation.

The recordings of the August 2023 OMERO workshop used Zoom to capture the presenter's screen as they walked through using the software. They have been cleaned up and edited down to 16 video segments and are available on the University of Arizona D2L system (D2L class link). PDF list of the workshop videos and a brief description of what topics each video covers.

Please email the team at RII-Omero@arizona.edu to request access to the D2L "course". (NOTE: the D2L site is only available to users with UA NetID logins)