If you have worked with image data for long you are probably aware that there are dozens of specialty file formats, many of which cannot be easily opened in commercial software. In addition, microscopy data has become more complex, with multiple focal planes, time points, locations, channels, and very large file sizes.
The NSF has had data management requirements for their grants for several years. Earlier this year the NIH added a data management and sharing requirement to all new NIH grants. OMERO is open-source software that the UA has recently made available which can help campus research labs with image data management. To assist interested users in getting started with OMERO we have scheduled a two-day, hands-on workshop for OMERO on August 3-4, 2023. We are bringing in the training team from the Open Microscopy group.
- Registration: We can’t do last minute walk-ins, we need people to register in advance (our maximum capacity is 50 participants), please use this Google form: Registration Form (email would be your UAnetID@arizona.edu)
- Date & Time: August 3-4, 2023, 9am-5pm, both days
- Cost: Free - a catered lunch will be provided as well as coffee & pastries in the morning.
- Location: Health Sciences Innovation Building (HSIB, https://map.arizona.edu/216), the room number will be shared with registered participants.
- Requirements: Participants are expected to bring their own laptop capable of getting on UA WiFi. This would be the ideal, but it might work if two people from the same group shared a laptop. Laptops will most likely need to have some additional software installed; further instructions will be sent to registered participants to allow them time to work with their IT teams to get the software installed before the workshop.
- Questions: email us at RIIemail@example.com
Using internal UA funding, the Data Science Institute has recently set up an Open Microscopy Environment file server (OMERO) to help faculty and their labs with image data management. The OMERO server uses the BioFormats plugin found in many open-source software packages to open proprietary files and convert them internally to OME-TIF so that (just about) any uploaded data can be viewed either through a web or desktop client. For more information on OMERO, see: https://datascience.arizona.edu/analytics-powerhouse/omero To get a quick look at the user interface, this 2 min (un-narrated) video will show a few of the features of the OMERO software. For a bit of context; both Canada and France are currently working on building their own national infrastructure for image data management using OMERO.
To clarify: The OMERO server is not intended to warehouse miscellaneous data like so many of the external drives that are floating around in research labs, it is not a “backup site”. The expectation is that the image data on OMERO will be curated, that information about the experiment performed, the sample and how it was prepared prior to imaging, the metadata from the microscope (if not automatic, then added by the user), and information regarding post-processing and/or analysis of the image data will be part of what is stored with the data. This is consistent with the NSF & NIH requirements.