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#bioimageanalysis — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #bioimageanalysis, aggregated by home.social.

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  1. 🚀 #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 🤗

    🌍 motila.readthedocs.io/en/lates

    #microglia #motility #Bioimageanalysis #Python

  2. 🚀 #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 🤗

    🌍 motila.readthedocs.io/en/lates

    #microglia #motility #Bioimageanalysis #Python

  3. 🚀 #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 🤗

    🌍 motila.readthedocs.io/en/lates

    #microglia #motility #Bioimageanalysis #Python

  4. 🚀 #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 🤗

    🌍 motila.readthedocs.io/en/lates

    #microglia #motility #Bioimageanalysis #Python

  5. 🚀 #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 🤗

    🌍 motila.readthedocs.io/en/lates

    #microglia #motility #Bioimageanalysis #Python

  6. #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.

    🌍 omio.readthedocs.io/en/latest/
    ⚙️ omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Python

  7. #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.

    🌍 omio.readthedocs.io/en/latest/
    ⚙️ omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Python

  8. #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.

    🌍 omio.readthedocs.io/en/latest/
    ⚙️ omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Python

  9. #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.

    🌍 omio.readthedocs.io/en/latest/
    ⚙️ omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Python

  10. #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.

    🌍 omio.readthedocs.io/en/latest/
    ⚙️ omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Python

  11. 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.

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  12. 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.

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  13. 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.

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  14. 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.

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  15. 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.

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  16. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  17. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  18. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  19. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  20. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/

    #BioimageAnalysis #Neuroscience #Python

  21. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/
    👨‍💻 github.com/FabrizioMusacchio/o

    #Microscopy #BioimageAnalysis #Python #OpenScience

  22. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/
    👨‍💻 github.com/FabrizioMusacchio/o

    #Microscopy #BioimageAnalysis #Python #OpenScience

  23. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/
    👨‍💻 github.com/FabrizioMusacchio/o

    #Microscopy #BioimageAnalysis #Python #OpenScience

  24. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/
    👨‍💻 github.com/FabrizioMusacchio/o

    #Microscopy #BioimageAnalysis #Python #OpenScience

  25. 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 ✌️

    🌍 omio.readthedocs.io/en/latest/
    👨‍💻 github.com/FabrizioMusacchio/o

    #Microscopy #BioimageAnalysis #Python #OpenScience

  26. 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:

    🌍 omio.readthedocs.io/

    🧵1/8

    #BioimageAnalysis

  27. 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:

    🌍 omio.readthedocs.io/

    🧵1/8

    #BioimageAnalysis

  28. 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:

    🌍 omio.readthedocs.io/

    🧵1/8

    #BioimageAnalysis

  29. 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:

    🌍 omio.readthedocs.io/

    🧵1/8

    #BioimageAnalysis

  30. 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:

    🌍 omio.readthedocs.io/

    🧵1/8

    #BioimageAnalysis

  31. 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?

    📝 doi.org/10.1242/jcs.264367

    #Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis

  32. 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?

    📝 doi.org/10.1242/jcs.264367

    #Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis

  33. 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?

    📝 doi.org/10.1242/jcs.264367

    #Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis

  34. 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?

    📝 doi.org/10.1242/jcs.264367

    #Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis

  35. 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?

    📝 doi.org/10.1242/jcs.264367

    #Neuroscience #Statistics #Biology #imageanalysis #Bioimaging #imaging #bioimageanalysis

  36. 🧠📐 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.

    🌍 doi.org/10.1038/s41586-026-105

    #Neuroscience #Neuroimmunology #BioimageAnalysis #AI

  37. 🧠📐 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.

    🌍 doi.org/10.1038/s41586-026-105

    #Neuroscience #Neuroimmunology #BioimageAnalysis #AI

  38. 🧠📐 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.

    🌍 doi.org/10.1038/s41586-026-105

    #Neuroscience #Neuroimmunology #BioimageAnalysis #AI

  39. 🧠📐 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.

    🌍 doi.org/10.1038/s41586-026-105

    #Neuroscience #Neuroimmunology #BioimageAnalysis #AI

  40. 🧠📐 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.

    🌍 doi.org/10.1038/s41586-026-105

    #Neuroscience #Neuroimmunology #BioimageAnalysis #AI

  41. 🎉 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

  42. 🎉 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

  43. 🎉 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

  44. 🎉 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

  45. 🎉 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