@will-j-moore.bsky.social
Reposted
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking.
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
December 8, 2025 at 9:48 AM
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking.
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
Reposted
Idr0168: Prediction of protein subcellular localization in single cells from www.nature.com/articles/s41... by Zhang et al. Images in idr0168 are OME-Zarrs converted by the submitter.
idr.openmicroscopy.org/search/?quer...
idr.openmicroscopy.org/search/?quer...
November 21, 2025 at 10:18 AM
Idr0168: Prediction of protein subcellular localization in single cells from www.nature.com/articles/s41... by Zhang et al. Images in idr0168 are OME-Zarrs converted by the submitter.
idr.openmicroscopy.org/search/?quer...
idr.openmicroscopy.org/search/?quer...
Reposted
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
November 21, 2025 at 9:29 AM
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
Reposted
So nice to see this!!!
I am still digesting all the info from the OME-NGFF hackathon last week.
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
November 19, 2025 at 8:33 PM
So nice to see this!!!
Reposted
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Python package managers: uv vs pixi?
When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I don’t hear much ab...
jacobtomlinson.dev
November 18, 2025 at 12:56 PM
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Reposted
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
Reposted
This week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)
November 20, 2024 at 10:31 PM
This week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)
Reposted
Been busy in Zürich für the last 24h or so. Talks have been great so far, and I have a talk too. Still find it weird to see my name on a poster.
November 11, 2025 at 11:17 AM
Been busy in Zürich für the last 24h or so. Talks have been great so far, and I have a talk too. Still find it weird to see my name on a poster.
Morning run to explore Zurich and grab breakfast
November 11, 2025 at 6:57 AM
Morning run to explore Zurich and grab breakfast
Reposted
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
Reposted
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Adventures in Code VII: getting started with napari – quantixed
quantixed.org
November 4, 2025 at 10:00 AM
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Another #OME-Zarr RFC, another implementation! Started a basic display of OME-Zarr Collections (RFC-8) in ome-ngff-validator at github.com/ome/ome-ngff...
October 31, 2025 at 10:52 AM
Another #OME-Zarr RFC, another implementation! Started a basic display of OME-Zarr Collections (RFC-8) in ome-ngff-validator at github.com/ome/ome-ngff...
Reposted
Today, napari users can’t fully leverage Xarray’s labeled metadata, as slider names, units & dimensions often get out of sync. That’s changing. At SciPy 2025, napari, Xarray & CellProfiler devs began a collab to build true metadata-aware visualization across sciences.
earthmover.io/blog/scienti...
earthmover.io/blog/scienti...
Scientific Data Visualization with Xarray and Napari - Earthmover
Ian Hunt-Isaak Xarray Community Developer Tim Monko Neuroscience PhD & napari community manager This blog was also published on the xarray blog and the napari blog. TL;DR Making Napari and Xarray work...
earthmover.io
October 29, 2025 at 5:53 PM
Today, napari users can’t fully leverage Xarray’s labeled metadata, as slider names, units & dimensions often get out of sync. That’s changing. At SciPy 2025, napari, Xarray & CellProfiler devs began a collab to build true metadata-aware visualization across sciences.
earthmover.io/blog/scienti...
earthmover.io/blog/scienti...
Reposted
The comedy Wildlife photography competition come at the perfect time each year www.comedywildlifephoto.com/gallery/fina...
These images are for viewing only and must not be copied :: Comedy Wildlife Photography Awards - Conservation through Competition
www.comedywildlifephoto.com
October 28, 2025 at 7:10 AM
The comedy Wildlife photography competition come at the perfect time each year www.comedywildlifephoto.com/gallery/fina...
Reposted
If you've ever worked with OME things, it is worth reading this update from Jason Swedlow on image.sc about the evolving OME governance. The TL;DR is that an interim leadership team has been assembled and new governance structures are coming sooner rather than later. forum.image.sc/t/ome-transi...
OME Transition-- Update
Dear All- Over the past two decades, OME has grown into a vibrant and global community dedicated to developing open standards, tools, and resources for the management, sharing, and analysis of micros...
forum.image.sc
October 22, 2025 at 4:28 AM
If you've ever worked with OME things, it is worth reading this update from Jason Swedlow on image.sc about the evolving OME governance. The TL;DR is that an interim leadership team has been assembled and new governance structures are coming sooner rather than later. forum.image.sc/t/ome-transi...
Reposted
Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. 🟥 ➡️ 🌎
October 22, 2025 at 9:24 AM
Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. 🟥 ➡️ 🌎
Those sample datasets are public, so you can try them yourselfs. Links can also be found at github.com/ome/ome-ngff...
October 20, 2025 at 1:02 PM
Those sample datasets are public, so you can try them yourselfs. Links can also be found at github.com/ome/ome-ngff...
The #OME-Zarr RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at github.com/will-moore/n.... Cool that you can offset T-dimension as well as XYZ!
October 20, 2025 at 1:00 PM
The #OME-Zarr RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at github.com/will-moore/n.... Cool that you can offset T-dimension as well as XYZ!
Reposted
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 11, 2025 at 1:30 PM
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Very nice! Your Affine Transform blog post is really neat and just what I needed right now 👍 for #OME-Zarr RFC-5. I also want to try out marimo and Web Assembly 😍
I'm happy to release into the wild my new professional and personal website marcodallavecchia.gitlab.io/web/
I finally found some time to reorganize ideas and redo the framework with @quarto.org
You can read my first blog post on the website here!
marcodallavecchia.gitlab.io/web/blog/web...
I finally found some time to reorganize ideas and redo the framework with @quarto.org
You can read my first blog post on the website here!
marcodallavecchia.gitlab.io/web/blog/web...
Personal & Professional Website – marcodallavecchia/web
my corner of the web
marcodallavecchia.gitlab.io
October 7, 2025 at 10:44 AM
Very nice! Your Affine Transform blog post is really neat and just what I needed right now 👍 for #OME-Zarr RFC-5. I also want to try out marimo and Web Assembly 😍
Reposted
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
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
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
September 15, 2025 at 5:26 PM
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
Reposted
What to do if you have extraordinary size data but no extraordinary local memory? 😱
At the @grcib2025.bsky.social, @joshmoore.bsky.social addressed this issue in the talk “When Data Doesn’t Fit – A Bioimaging Story from Files to FAIR”.
👉 Interested? zenodo.org/records/1708...
At the @grcib2025.bsky.social, @joshmoore.bsky.social addressed this issue in the talk “When Data Doesn’t Fit – A Bioimaging Story from Files to FAIR”.
👉 Interested? zenodo.org/records/1708...
September 16, 2025 at 7:54 AM
What to do if you have extraordinary size data but no extraordinary local memory? 😱
At the @grcib2025.bsky.social, @joshmoore.bsky.social addressed this issue in the talk “When Data Doesn’t Fit – A Bioimaging Story from Files to FAIR”.
👉 Interested? zenodo.org/records/1708...
At the @grcib2025.bsky.social, @joshmoore.bsky.social addressed this issue in the talk “When Data Doesn’t Fit – A Bioimaging Story from Files to FAIR”.
👉 Interested? zenodo.org/records/1708...