Tessera

Image Cooperative

@image.coop

We are a cooperative of imaging scientists dedicated to advancing open standards and open source technology in scientific image data analysis, storage, and dissemination. https://image.coop

14 Posts131 Follower 0 Folgt

eurobioimaging.bsky.social @eurobioimaging.bsky.social · 3w ago

At the next #NGFFCafe, Marvin Albert (ETH Zurich) will present 𝗺𝘂𝗹𝘁𝗶𝘃𝗶𝗲𝘄-𝘀𝘁𝗶𝘁𝗰𝗵𝗲𝗿, a Python package for scalable stitching/alignment/fusion of multi-view, tiled & multimodal image acquisitions. Join us! 🗓️ Thursday, July 30 🕚️ 11 am CEST 📍 Online Register⤵️ us02web.zoom.us/meeting/regi...

John Bogovic @bogovicj.bsky.social · 3w ago

It's an exciting day for #Fiji users! Now read and write @zarr.dev v3 and #OMEZarr v0.5. Don't want a million tiny files in your #zarr? Shard that sucker! Read the details here forum.image.sc/t/fiji-can-r...

Fiji can read and write Zarr3 & OME-Zarr v0.5 (new N5 release!)

Updating your Fiji-Latest installation will give you the newest versions of the N5 library, enabling OME-Zarr v0.5 / Zarr v3 support with sharding! What's new? Reading zarr 3 datasets (sharded and u...

forum.image.sc

Image Cooperative @image.coop · last mo.

Earlier in June, we had our first in-person meeting at @embl.org (thank you for hosting us!), joined by representatives from Glencoe, Fideus Labs, @gerbi-gmb.de, and @scalableminds.com (+Dundee & Janelia on zoom) to start our OME-Zarr 1.0 project. More details to come, but it was fun and productive!

OME-Zarr collaborators having lunch together at the EMBL cafeteria

OME-Zarr working group discussing in a meeting room

Juan talking about Image Cooperative at an EMBL seminar room

hackathon participants having dinner in Heidelberg

Image Cooperative @image.coop · last mo.

We're excited to help organize the OME-Zarr Office Hours with a new rotating schedule starting today! 🎉 Whether you're using OME-Zarr today or just curious to learn more, we'd love to see you there. 📅 Full schedule: ngff.openmicroscopy.org/community

White text on dark blue saying, "OME-ZARR OFFICE HOURS. New schedule, more time zones! Our office hours now rotate over 3 time zones so more of our community can join in. See the full schedule and
add to your calendar: ngff.openmicroscopy.org/community/#office-hours -- Let's make OME-Zarr more accessible--together! 👋🏼"

A graphic shows the various time zones -- Americas, Asia-Pacific, and Europe/Africa in green, light blue and purple -- with arrows showing the rotation.

Image Cooperative @image.coop · 2mo ago

Keeping track of OME-Zarr support across the ecosystem isn't always easy. Over the past few weeks, we've been speaking with stakeholders about experiences, successes, and remaining gaps. Here is our snapshot of where things stand and where effort may be most valuable next: image.coop/blog/posts/2...

OME-Zarr Pulse Check: Spec, Tooling, and Community – Image Cooperative

Feedback and insights from chatting to the community and analysing ecosystem data over the last six weeks.

image.coop

Image Cooperative @image.coop · 2mo ago

Image Coop at the @embl.org chicken coop! Thanks to @erickratamero.com for hosting us, for the tour, and for the photo!

The Image Cooperative team (left to right: Draga Doncila Pop, Eric Perlman, Josh Moore, Juan Nunez-Iglesias, Kevin Yamauchi) helping feed the chickens at the EMBL chicken coop. Photo by Erick Ratamero who was on chicken duty at the time and was also kindly hosting us.

Image Cooperative @image.coop · 2mo ago

Some initial results from the live survey at the recent #OME-Zarr Community Call for you to ponder over the weekend. Thoughts, as always, welcome! 🤔

Slide titled "What keeps you engaged with OME-Zarr?" with colored boxes sized to match the number of responses:

## Community (15)
- Great people!
- Delightful people
- Very knowledgable approachable people in the community
- Job, but also exciting to support the community
- People care
- Friendly community
- open communication with the community
- Awesome community
- The community x7

## Value & Trajectory (13)
- moving towards 1.0
- we're almost there :)
- The momentum
- It is the future
- hope
- Love the vision
- finally having the One True Format
- Format is useful and things are happening!
- very promising to handle large data in the future, nothing else seems to provide this
- Data is too big for anything else
- Better format to handle big data
- Potential to solve difficult/modern data problems.
- Obvious value of ome zarr

## Outreach (4)
- very good outreach!
- I'm new here but I will be back! :)
- Curiosity
- Staying updated

## Open (2)
- Open
- Open source

## Flexible (2)
- Versatile
- Flexible

## Misc. (9)
- Useful
- Fair data
- Right technology
- Making hard problems easier
- Need to be able to support end users
- I want to be able to access the benefits
- Scverse uses OME-Zarr as a backbone for Spatialdata object
- "pressure" from the repos, as the only accepted format
- The fame and money

Slide titled "What keeps you engaged with OME-Zarr?" with colored boxes matching the number of responses.

# Large data / Scalability (13)
- Dealing with large images
- Large data support
- large data handling
- Sharing large datasets
- scalability x4
- Big data x3
- Scalable x2

## Cloud native (9)
- Works in the cloud and locally
- Cloud support
- Cloud data native
- Cloud native brick storage
- cloud native x3
- Native cloud support x2

## Remote access (5)
- Streaming support x2
- streamable
- deposit data once and everything else just uses the S3-URL
- deposit somewhere once, access/index it from everywhere

## Community (5)
- It is represented by an international community
- Large Community support and buy in
- Community support
- good community support
- community driven

## Performance (5)
- Efficient storage, transfer and sharing
- Lazy Loading
- Rapid loading over network
- Parallel IO
- Easy browsing and parallel computing on large datasets

## Standardisation (3)
- Standardisation x2
- Standardization

## Chunking (3)
- Chunking
- Data in chunks
- Multiscale, chunked access

## Flexible (3)
- Flexible x2
- Extensible

## Open (3)
- Openness x2
- Open

## FAIRness (2)
- FAIRness x2

## Misc. (8)
- Multimodal images
- Independence on compute hardware
- Interoperability
- Remote visualization
- Easy visualisation
- Human readable
- vendor agnostic
- growing acceptance

Slide titled "What are the drawbacks of OME-Zarr?" with colored boxes sized to match the number of entries:

## Tooling Support (14)
- Tools have unclear incompatibilities
- Lack of generalised processing tools
- Too many libraries with different features
- lack of a single cannonical library for python
- "unclear tool eco-system / unclear features / important features missing"
- Most easy to use tools focus on visualisation only, not processing
- not yet enough interoperability with different tools, but it gets more
- What tool and version supports what and how to choose reasonable settings
- Easy to Load in FIJI
- Fiji support
- Using traditional Fiji 2D algorithms on OME Zarr is not efficient
- OMERObility
- OMERO support incomplete
- Traditional orthogonal 3D viewer is still lacking

## Evolving spec. (13)
- evolving spec x4
- Not stable enough yet
- Unstable spec
- Not finished
- not stable
- Not meeting all requirements yet
- Changing specification
- Might there be massive (potentially breaking) changes in future?
- Missing metadata
- Missing flexibility

## User accessibility (9)
- Too technical x2
- Complexity x2
- user comfort
- Difficult to access for end users
- Hard to use if not computationally comfortable
- giving access to s3 to biologists
- Not entirely supporting biologists

## File systems (7)
- Too many files
- Many small files
- Many files
- inodes
- Amount of files
- problem on traditional filesystem
- HPC use

## Version confusion (4)
- Fracture between Zarr v2 v3, omezarr v4, v5
- confusion with versions of zarr and versions of ome-ngff
- Hard to know which tool and version supports what
- Is ome NGFF equal to ome.zarr?

## Infrastructure (4)
- Authentication
- lack of good data management tools (auth, groups, etc)
- lack of object storage infrastructure
- Network performance/overhead

## Compression (3)
- No RGB compression
- No lossy compression
- Codec support

## Vendor support (3)
- No vendor support
- Missing features for vendors
- not y…

Image Cooperative @image.coop · 2mo ago

Getting to know who's in the room at the first session of the #OME-Zarr Community Call. If you missed it, join for the second session to share your thoughts. Let's grow that 'curious' bubble! 🫧 forum.image.sc/t/join-us-fo...

Screenshot of a mentimeter poll titled, "How are you involved with OME-Zarr? Select all that apply". The results are:

3 - Curious/not actively using OME-Zarr. 12 - Tool developer. 11 - Spec contributor. 12 - OME-Zarr data user/Analyst. 6 - Other

Image Cooperative @image.coop · 3mo ago

We want to hear from you about your experience using the OME-Zarr ecosystem and how we can improve it! We are joining the upcoming OME-NGFF community call to introduce ourselves to the community and to collect your feedback (May 26, 9AM and 5PM CET). See you there! forum.image.sc/t/join-us-fo...

Join us for the next OME-NGFF Community Call on Tuesday May 26, 2026 9:00 CET and 17:00 CET!

Dear all, We are delighted to announce our Q2 OME-NGFF Community Call to be held on Tuesday May 26! As usual, we will repeat the agenda over two time slots to welcome participants from everywhere aro...

forum.image.sc

Tiago Lubiana @tiagolubiana.bsky.social · 3mo ago

great first presentation of the @image.coop, by @perlman.bsky.social exciting stuff! #GIDE2026

Image Cooperative @image.coop · 3mo ago

Member Eric Perlman takes the stage at @embl.org to announce our launch as an international worker co-op for #OSS scientific imaging software. First task supported by @biohub.org is accelerating #OMEZarr towards a 1.0 alpha early 2027. Stay tuned! image.coop #GIDE2026 @gideproject.bsky.social

A screenshot of Eric's title slide, saying "The role of COOPeration in global imaging. Eric Perlman. Member, Image Cooperative" in Atkinson Hyperlegible font in black on white. The footer is a subtle pink-to-green bar with the hexagonal ball as a separator. The text in the footer says "Image Cooperative Ltd."

A photo of Eric behind the mic at EMBL with the first slide as described in the other image being shown by the projector.

Image Cooperative @image.coop · 3mo ago

Where better to hear the community's thoughts on #OMEZarr!

NFDI4BIOIMAGE@nfdi4bioimage.bsky.social · 3mo ago

Day 1 at #OME2026 is coming to an end with stimulating discussions during the poster session. It's been a wonderful first conference day. Looking forward to tomorrow with highlights including workshops and our keynote speaker Carole Goble. Stay tuned.

Image Cooperative @image.coop · 3mo ago

Thrilled to join #ome2026! Reach out to Eric or Josh if you want to chat.

German BioImaging@gerbi-gmb.de · 3mo ago

The 19th OME Meeting just kicked off in Düsseldorf! So happy to welcome this wonderful community to @hhu.de together with @nfdi4bioimage.bsky.social and the @openmicroscopy.org Team — really looking forward to the days ahead. 😊 Join online: gerbi-gmb.de/event/ome-20... #OME2026 #NFDI4BIOIMAGE #OME

Josh Moore @joshmoore.bsky.social · 4mo ago

Really excited to finally share this more widely. This is exactly the kind of work we hoped the cooperative could support—helping turn strong community momentum around #OMEZarr into something more coordinated and sustained. Very curious to hear what people think.

Image Cooperative@image.coop · 4mo ago

Our first project is live. ✨ With support from @biohub.org, @image.coop is coordinating work across the #OMEZarr community to help move the standard toward 1.0—supporting both implementation and the coordination needed to get there. More details in our latest post: image.coop/blog/posts/2...

Image Cooperative @image.coop · 4mo ago

Image Cooperative’s first order of business: helping push the OME-Zarr standard forward – Image Cooperative

Announcing our first partnership and how we hope to contribute to OME-Zarr

image.coop

Image Cooperative @image.coop · 5mo ago

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...