#bioimageanalysis — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #bioimageanalysis, aggregated by home.social.
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🚀Another #MotilA update this morning: v1.1.3 brings optional #CSV & #YAML export, which makes MotilA less reliant on proprietary file formats. … And: MotilA got its first logo 🤗
🌍 https://motila.readthedocs.io/en/latest/changelog.html#motila-v1-1-3
#BioimageAnalysis #microglia #motility #Python https://mastodon.social/@FabMusacchio/117077490957638600
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🚀Another #MotilA update this morning: v1.1.3 brings optional #CSV & #YAML export, which makes MotilA less reliant on proprietary file formats. … And: MotilA got its first logo 🤗
🌍 https://motila.readthedocs.io/en/latest/changelog.html#motila-v1-1-3
#BioimageAnalysis #microglia #motility #Python https://mastodon.social/@FabMusacchio/117077490957638600
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🚀 #MotilA now runs with #OMIO!
Today’s version release v1.1.2 adds much more flexible image I/O: #TIFF/ OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO and normalized to #OME-compliant TZCYX axis-order, automatically. So, no more manual axis reordering before analysis 🤗
🌍 https://motila.readthedocs.io/en/latest/changelog.html#motila-v1-1-2
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🚀 #MotilA now runs with #OMIO!
Today’s version release v1.1.2 adds much more flexible image I/O: #TIFF/ OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO and normalized to #OME-compliant TZCYX axis-order, automatically. So, no more manual axis reordering before analysis 🤗
🌍 https://motila.readthedocs.io/en/latest/changelog.html#motila-v1-1-2
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#OMIO is meanwhile at v0.2.9 🚀
The main focus this past week was making #Thorlabs RAW handling more robust: Better #XML/ #YAML #metadata fallback, support for batch-friendly error handling, and clearer diagnostics when metadata doesn’t match the RAW data.
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-9
⚙️ https://omio.readthedocs.io/en/latest/usage_file_format_supported.html#reading-thorlabs-raw-files -
#OMIO is meanwhile at v0.2.9 🚀
The main focus this past week was making #Thorlabs RAW handling more robust: Better #XML/ #YAML #metadata fallback, support for batch-friendly error handling, and clearer diagnostics when metadata doesn’t match the RAW data.
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-9
⚙️ https://omio.readthedocs.io/en/latest/usage_file_format_supported.html#reading-thorlabs-raw-files -
Today’s release of #OMIO (v0.2.6) is again a small update, but it brings memory-efficient OME-TIFF writing for Zarr-backed workflows. When imwrite receives a disk-cached #Zarr array, OMIO now streams it plane by plane instead of materializing the full store in RAM.
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-6
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Today’s release of #OMIO (v0.2.6) is again a small update, but it brings memory-efficient OME-TIFF writing for Zarr-backed workflows. When imwrite receives a disk-cached #Zarr array, OMIO now streams it plane by plane instead of materializing the full store in RAM.
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-6
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Today's release of #OMIO (v0.2.5) is just a small update, but brings a useful option: configurable disk-cache locations for imread(). Ideal when large #microscopy files live e.g. on a server, while you want OMIO's disk-backed #Zarr cache stored locally for smoother and faster processing and reuse ✌️
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-5
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Today's release of #OMIO (v0.2.5) is just a small update, but brings a useful option: configurable disk-cache locations for imread(). Ideal when large #microscopy files live e.g. on a server, while you want OMIO's disk-backed #Zarr cache stored locally for smoother and faster processing and reuse ✌️
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-5
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#OMIO is now at version v0.2.4. This maintenance release brings cleaner API docs, disk-backed empty image creation, and a more convenient #napari opener with automatic layer names, custom channel labels, and configurable blending ✌️
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-4
📚 https://omio.readthedocs.io/en/latest/usage_template_functions.html#creating-empty-images-as-on-disk-zarr-arrays
📚 https://omio.readthedocs.io/en/latest/usage_core_functions.html#opening-images-in-napari-and-metadata-modification -
#OMIO is now at version v0.2.4. This maintenance release brings cleaner API docs, disk-backed empty image creation, and a more convenient #napari opener with automatic layer names, custom channel labels, and configurable blending ✌️
🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-4
📚 https://omio.readthedocs.io/en/latest/usage_template_functions.html#creating-empty-images-as-on-disk-zarr-arrays
📚 https://omio.readthedocs.io/en/latest/usage_core_functions.html#opening-images-in-napari-and-metadata-modification -
I just pushed #OMIO to version v0.2.2. You can now reuse existing disk-backed #Zarr caches instead of rebuilding them every time an image is opened. OMIO stores cache metadata directly in the Zarr store and validates compatibility automatically before reuse ✌️
🌍 https://omio.readthedocs.io/en/latest/usage_large_files.html#reuse-an-existing-on-disk-omio-cache
👨💻 https://github.com/FabrizioMusacchio/omio -
I just pushed #OMIO to version v0.2.2. You can now reuse existing disk-backed #Zarr caches instead of rebuilding them every time an image is opened. OMIO stores cache metadata directly in the Zarr store and validates compatibility automatically before reuse ✌️
🌍 https://omio.readthedocs.io/en/latest/usage_large_files.html#reuse-an-existing-on-disk-omio-cache
👨💻 https://github.com/FabrizioMusacchio/omio -
#OMIO is fully #OpenSource:
👨💻 https://github.com/FabrizioMusacchio/omio/
Documentation, tutorials, example data, and a #bioRxiv #preprint are also available:
📚 https://omio.readthedocs.io/en/latest/
📈 https://zenodo.org/records/18078231
📑 https://doi.org/10.64898/2026.06.09.731118#BioimageAnalysis #Microscopy #Neuroscience
🧵7/8
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#OMIO is fully #OpenSource:
👨💻 https://github.com/FabrizioMusacchio/omio/
Documentation, tutorials, example data, and a #bioRxiv #preprint are also available:
📚 https://omio.readthedocs.io/en/latest/
📈 https://zenodo.org/records/18078231
📑 https://doi.org/10.64898/2026.06.09.731118#BioimageAnalysis #Microscopy #Neuroscience
🧵7/8
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If you work with #microscopy images 🧠🔬 in #Python 🐍👨💻, you may know the situation: Different file formats, readers, axis conventions, metadata structures... At least I found this increasingly frustrating. So I built #OMIO (Open Microscopy Image I/O), a unified microscopy image reader & writer for #Python:
🌍 https://omio.readthedocs.io/
🧵1/8
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If you work with #microscopy images 🧠🔬 in #Python 🐍👨💻, you may know the situation: Different file formats, readers, axis conventions, metadata structures... At least I found this increasingly frustrating. So I built #OMIO (Open Microscopy Image I/O), a unified microscopy image reader & writer for #Python:
🌍 https://omio.readthedocs.io/
🧵1/8
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In the latest issue of #JCellSci, with Stefania Marcotti, Lina Gerontogianni, Gavin Kelly, & David J. Barry, a reanalysis of images from the #IDR to answer the age-old question:
How do you tell #statistical #significance from #biological significance?
📝 https://doi.org/10.1242/jcs.264367
#Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis
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In the latest issue of #JCellSci, with Stefania Marcotti, Lina Gerontogianni, Gavin Kelly, & David J. Barry, a reanalysis of images from the #IDR to answer the age-old question:
How do you tell #statistical #significance from #biological significance?
📝 https://doi.org/10.1242/jcs.264367
#Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis
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🧠📐 Kaltenecker et al present #MouseMapper, that combines whole-body tissue clearing, #lightsheet #imaging and foundation-model-based #DeepLearning to quantify nerves, immune cells & 31 organs/tissues across entire #mouse bodies.
Applied to diet-induced #obesity, it revealed reduced nerve density, infraorbital trigeminal nerve defects, impaired whisker sensing, & body-wide inflammatory CD68⁺ immune-cell clustering.
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🧠📐 Kaltenecker et al present #MouseMapper, that combines whole-body tissue clearing, #lightsheet #imaging and foundation-model-based #DeepLearning to quantify nerves, immune cells & 31 organs/tissues across entire #mouse bodies.
Applied to diet-induced #obesity, it revealed reduced nerve density, infraorbital trigeminal nerve defects, impaired whisker sensing, & body-wide inflammatory CD68⁺ immune-cell clustering.
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🎉 Announcing the naPLari hackathon in Kraków, Poland 🇵🇱, July 24–29 2026, after EuroSciPy!
Hack on napari, join deep dives, meet the team. All experience levels welcome!
📝 Register by July 1: napari.typeform.com/naplari-hack
#napari #ScientificPython #OpenSource #EuroSciPy #BioImageAnalysis
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🎉 Announcing the naPLari hackathon in Kraków, Poland 🇵🇱, July 24–29 2026, after EuroSciPy!
Hack on napari, join deep dives, meet the team. All experience levels welcome!
📝 Register by July 1: napari.typeform.com/naplari-hack
#napari #ScientificPython #OpenSource #EuroSciPy #BioImageAnalysis
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1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @[email protected] from my team! #napari #bioimageanalysis #MCP @biohub
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1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @[email protected] from my team! #napari #bioimageanalysis #MCP @biohub
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11/ 🔬🧪 Try it today! pip install napari-chatgpt — GitHub: github.com/royerlab/napari-chatgpt — Paper: doi.org/10.1038/s41592-024-02310-w #Omega #napari #AI #BioImageAnalysis
GitHub - royerlab/napari-chatg... -
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!
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#bioimageanalysis wouldn't be the same without all the great RSEs who make our tools and keep them working! Great paper on this from a couple of years ago linked below - if there's a tool that makes your life easier, think about taking a few minutes today to thank the person or people who make it!
RE: https://bsky.app/profile/did:plc:okkgjibnf4hzx2b7k2avhznm/post/3m2qli6skfb2x
Frontiers | Better research so... -
If you would like to attend a microscopy or bioimage analysis training course in the next 6 months but don’t have funding, check out our Microscopy Training Grant from @J_Cell_Sci and @focalplane_jcs.
Next deadline: 6 June 2025
https://www.biologists.com/grants/jcs-focalplane-training-grants/
#Microscopy #BioimageAnalysis #Bioimage #Biology #Training #Grants
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If you would like to attend a microscopy or bioimage analysis training course in the next 6 months but don’t have funding, check out our Microscopy Training Grant from @J_Cell_Sci and @focalplane_jcs.
Next deadline: 6 June 2025
https://www.biologists.com/grants/jcs-focalplane-training-grants/
#Microscopy #BioimageAnalysis #Bioimage #Biology #Training #Grants
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BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
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If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2) forms.gle/C8dUpg8qZkbD... #bioimaging #microscopy #bioimageanalysis
Open Source Bioimage Analysis ... -
Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis
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Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)
Ask Erin, Dear Beth -
If, hypothetically, a person were trying to set up a career panel series for bioimage analysis, what kinds of roles (or specific people) would you want to hear more about? Hypothetical nominations of all stripes welcome :) #bioimageanalysis
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Workshop on True Image Deconvolution, Restoration, and Analysis
When: March 13th, 2025 – 3 days from now.
2 hours long: 14:30 - 16:30 CET
Where: online, via zoom.
Program: https://www.crg.eu/en/event/workshop-true-image-deconvolution-restoration-and-analysis
Registration: https://apps.crg.es/content/internet/events/webforms/workshop-true-image-deconvolution-restoration-and-analysis
#BioimageAnalysis #PSF #deconvolution #ImageProcessing #microscopy
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Workshop on True Image Deconvolution, Restoration, and Analysis
When: March 13th, 2025 – 3 days from now.
2 hours long: 14:30 - 16:30 CET
Where: online, via zoom.
Program: https://www.crg.eu/en/event/workshop-true-image-deconvolution-restoration-and-analysis
Registration: https://apps.crg.es/content/internet/events/webforms/workshop-true-image-deconvolution-restoration-and-analysis
#BioimageAnalysis #PSF #deconvolution #ImageProcessing #microscopy
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We're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!
Software engineering intern - ... -
Nice shout-out to #opensource #microscopy and #imageanalysis #bioimageanalysis software at #CZIImaging #ImagingTheFuture.
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This 3D image stack deconvolution tool looks super useful for #bioimageanalysis
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
Wernersson et al., Nature Methods 2024
https://doi.org/10.1038/s41592-024-02294-7Github: https://github.com/elgw/deconwolf/
Program: https://deconwolf.fht.org/ -
As academic #BioImageAnalysis jobs in Australia go, this one is pretty good: Microscopy Platform Applications Specialist at UniMelb Biological Optical Microscopy Platform.
https://jobs.unimelb.edu.au/caw/en/job/916889
The BOMP team is very nice, and continuing positions are really hard to find in Oz right now. (I do not have one.) Advertised at Academic Level A (geared at someone recently out of PhD).
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I'm sharing in this world the published tutorial from Robert Haase entitled “Generative Artificial Intelligence for Bio-image Analysis” from the #I2K202 conference on October 17.
Link to the YouTube video 👇
https://youtu.be/gLziaMjM3LM?si=JodImBcWyoYi6MXH -
Research Associate in Bioimage Analysis / Developmental Biology @ErikClark
University of Cambridge
Analyse imaging data from fruit fly embryos and solve long standing mysteries of developmental patterning: #BioimageAnalysis postdoc, Cambridge, UK.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-cambridge-27778-re...
https://jobrxiv.org/job/university-of-cambridge-27778-research-associate-in-bioimage-analysis-developmental-biology/?feed_id=65194