#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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🚀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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🚀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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🚀 #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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🚀 #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 -
#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 -
#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 (v0.2.6) 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 (v0.2.6) 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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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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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 -
#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 -
#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 -
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 -
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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#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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#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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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
-
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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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
-
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
-
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.
-
🧠📐 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.
-
🧠📐 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.
-
🧠📐 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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🎉 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
-
🎉 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