Josh Moore
@joshmoore.bsky.social
Technical Director – @gerbi-gmb.de | Standardizing open bioimaging data infrastructure
TA1 lead for @nfdi4bioimage.bsky.social
#OSS Maintainer for @openmicroscopy.org and @zarr.dev
TA1 lead for @nfdi4bioimage.bsky.social
#OSS Maintainer for @openmicroscopy.org and @zarr.dev
Shock slide of the first @nfdi.de workshop on #OverallArchitecture" 🤯 Marius Politze of #MatWerk sharing the breadth & depth of tools & services in use.
November 26, 2025 at 2:51 PM
Shock slide of the first @nfdi.de workshop on #OverallArchitecture" 🤯 Marius Politze of #MatWerk sharing the breadth & depth of tools & services in use.
Reposted by Josh Moore
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
November 20, 2025 at 1:03 PM
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
Reposted by Josh Moore
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵
1/14 🧵
November 17, 2025 at 1:24 PM
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵
1/14 🧵
Reposted by Josh Moore
Greetings from NFDI4Bioimage Task Area Leader Björn Grüning at the #EOSCSymposium2025, which is taking place from November 3 to 5 at Brussels. At the conference, Björn Grüning presents the #Galaxy use case, which is one of the first #EOSC candidate use cases.
👉 gxy.io/eosc25
Picture: Nicolas Lobet
👉 gxy.io/eosc25
Picture: Nicolas Lobet
November 5, 2025 at 12:13 PM
Greetings from NFDI4Bioimage Task Area Leader Björn Grüning at the #EOSCSymposium2025, which is taking place from November 3 to 5 at Brussels. At the conference, Björn Grüning presents the #Galaxy use case, which is one of the first #EOSC candidate use cases.
👉 gxy.io/eosc25
Picture: Nicolas Lobet
👉 gxy.io/eosc25
Picture: Nicolas Lobet
Reposted by Josh Moore
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Reposted by Josh Moore
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
September 19, 2025 at 7:35 AM
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Reposted by Josh Moore
Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org
@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
September 18, 2025 at 7:23 AM
Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org
@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
Reposted by Josh Moore
Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...
September 18, 2025 at 9:42 AM
Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...
Reposted by Josh Moore
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
September 16, 2025 at 7:46 AM
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
Reposted by Josh Moore
🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
September 15, 2025 at 9:57 AM
🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
Reposted by Josh Moore
🚀 Registration is open for BioHackathon Germany 2025! Join us 1–5 Dec in Walsrode for hands-on projects, networking, and innovation in #bioinformatics. 🧬🤝
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon
September 3, 2025 at 8:55 AM
🚀 Registration is open for BioHackathon Germany 2025! Join us 1–5 Dec in Walsrode for hands-on projects, networking, and innovation in #bioinformatics. 🧬🤝
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon
Reposted by Josh Moore
Julia Thönnißen from @fz-juelich.de demonstrates how large-scale 3D imaging data from neuroscience research can be handled & analyzed without the need for data duplication. Leveraging #OME-Zarr, the #tiamat tool developed at FZJ enables seamless work at scale. @nfdi4bioimage.bsky.social #CoRDI2025
August 28, 2025 at 8:58 AM
Julia Thönnißen from @fz-juelich.de demonstrates how large-scale 3D imaging data from neuroscience research can be handled & analyzed without the need for data duplication. Leveraging #OME-Zarr, the #tiamat tool developed at FZJ enables seamless work at scale. @nfdi4bioimage.bsky.social #CoRDI2025
Reposted by Josh Moore
We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊
📄 joss.theoj.org/papers/10.2110… (1/3)
📄 joss.theoj.org/papers/10.2110… (1/3)
ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets
Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882
joss.theoj.org
August 15, 2025 at 1:07 PM
We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊
📄 joss.theoj.org/papers/10.2110… (1/3)
📄 joss.theoj.org/papers/10.2110… (1/3)
Reposted by Josh Moore
Are you using Zarr (or want to know more)? Join us in #Rome for Zarr Adopter Days on Oct 16-17! This is a great chance to learn from implementers, get hands-on support & collaborate w/ the @stacspec.bsky.social sprint folks. Register now to save your spot! zarr-summit-2025.netlify.app
August 19, 2025 at 6:39 PM
Are you using Zarr (or want to know more)? Join us in #Rome for Zarr Adopter Days on Oct 16-17! This is a great chance to learn from implementers, get hands-on support & collaborate w/ the @stacspec.bsky.social sprint folks. Register now to save your spot! zarr-summit-2025.netlify.app
Reposted by Josh Moore
You are an OME-Zarr developer yourself? Join us at the hackathon! Help push OME-Zarr towards 1.0, work on RFCs to the spec, contribute to tooling in Java or Python or build workflows using OME-Zarrs.
Find out more & apply to the hackathon here: biovisioncenter.notion.site/2025-OME-NGF...
Find out more & apply to the hackathon here: biovisioncenter.notion.site/2025-OME-NGF...
2025 OME-NGFF Workflows Hackathon | Notion
Date: November 12th - 14th, 2025
biovisioncenter.notion.site
August 25, 2025 at 9:07 AM
You are an OME-Zarr developer yourself? Join us at the hackathon! Help push OME-Zarr towards 1.0, work on RFCs to the spec, contribute to tooling in Java or Python or build workflows using OME-Zarrs.
Find out more & apply to the hackathon here: biovisioncenter.notion.site/2025-OME-NGF...
Find out more & apply to the hackathon here: biovisioncenter.notion.site/2025-OME-NGF...
Reposted by Josh Moore
August 29, 2025 at 7:11 AM
Reposted by Josh Moore
How to make bioimage analysis workflows #FAIR? Riccardo Massei shows how to use efficient RDM & analysis pipelines in #Galaxy. As a @nfdi4bioimage.bsky.social Data Steward, Riccardo supports the community with expertise in data handling for high-content screening, image analysis & more. #CoRDI2025
August 27, 2025 at 8:15 AM
How to make bioimage analysis workflows #FAIR? Riccardo Massei shows how to use efficient RDM & analysis pipelines in #Galaxy. As a @nfdi4bioimage.bsky.social Data Steward, Riccardo supports the community with expertise in data handling for high-content screening, image analysis & more. #CoRDI2025
Reposted by Josh Moore
Find Robert Wagner on the ground floor level or C.A.R.L at the #CoRDI2025 conference to learn how #OMERO helps with #FAIR data management in the field of low-temperature plasma science. @inpgreifswald.bsky.social @nfdi4bioimage.bsky.social
August 27, 2025 at 8:01 AM
Find Robert Wagner on the ground floor level or C.A.R.L at the #CoRDI2025 conference to learn how #OMERO helps with #FAIR data management in the field of low-temperature plasma science. @inpgreifswald.bsky.social @nfdi4bioimage.bsky.social
Reposted by Josh Moore
Poster Session at #CoRDI2025. Here is @joshmoore.bsky.social presenting how cloud-ready next-generation file formats like #OME-Zarr enable federated repositories with large N-dimensional arrays at peta-scale.
#OME-NGFF @nfdi4bioimage.bsky.social
Find the poster on C.A.R.L level 2 @rwth.bsky.social
#OME-NGFF @nfdi4bioimage.bsky.social
Find the poster on C.A.R.L level 2 @rwth.bsky.social
August 27, 2025 at 7:41 AM
Poster Session at #CoRDI2025. Here is @joshmoore.bsky.social presenting how cloud-ready next-generation file formats like #OME-Zarr enable federated repositories with large N-dimensional arrays at peta-scale.
#OME-NGFF @nfdi4bioimage.bsky.social
Find the poster on C.A.R.L level 2 @rwth.bsky.social
#OME-NGFF @nfdi4bioimage.bsky.social
Find the poster on C.A.R.L level 2 @rwth.bsky.social
Reposted by Josh Moore
Once is an exception, twice is a trend, thrice is a tradition!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
We're happy to announce the 2025 International OME-NGFF workshop 🎉
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
August 25, 2025 at 1:50 PM
Once is an exception, twice is a trend, thrice is a tradition!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
Reposted by Josh Moore
We're happy to announce the 2025 International OME-NGFF workshop 🎉
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
August 25, 2025 at 9:07 AM
We're happy to announce the 2025 International OME-NGFF workshop 🎉
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
Reposted by Josh Moore
Zarr is hiring again! Build scalable bioimaging solutions, collaborate globally, and join the Friedrich Miescher Institute for Biomedical Research as a Computational Scientist or Research Software Engineer
www.fmi.ch/education-ca...
www.fmi.ch/education-ca...
July 16, 2025 at 6:26 PM
Zarr is hiring again! Build scalable bioimaging solutions, collaborate globally, and join the Friedrich Miescher Institute for Biomedical Research as a Computational Scientist or Research Software Engineer
www.fmi.ch/education-ca...
www.fmi.ch/education-ca...
Reposted by Josh Moore
🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.
We have an open #opportunity for a BioImage Analyst to join our team! This is an excellent role for a problem solver with an empathetic, collaborative mentality who enjoys partnering with interdisciplinary scientists. Read more and apply here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
BioImage Analyst
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute’s Janelia Research Campus is a pio...
hhmi.wd1.myworkdayjobs.com
February 13, 2025 at 12:17 AM
🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.
Who does microscopy and has never heard of Bio-Formats? You probably used it anyway
August 6, 2025 at 3:39 PM
Reposted by Josh Moore
Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)!
More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥
More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥
Funded Projects - swissuniversities
www.swissuniversities.ch
July 21, 2025 at 7:29 AM
Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)!
More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥
More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥