Microscopy and astronomy
- Multichannel OME-Zarr and OME-TIFF: channel contrast, z-slices, time points
- Draw regions or click cells to classify them, export GeoJSON that QuPath reads
- FITS cutouts with science/reference/difference triplets for vetting transients
- Multichannel OME-Zarr and OME-TIFF: channel contrast, z-slices, time points
- Draw regions or click cells to classify them, export GeoJSON that QuPath reads
- FITS cutouts with science/reference/difference triplets for vetting transients
October 29, 2026 at 2:37 AM
Microscopy and astronomy
- Multichannel OME-Zarr and OME-TIFF: channel contrast, z-slices, time points
- Draw regions or click cells to classify them, export GeoJSON that QuPath reads
- FITS cutouts with science/reference/difference triplets for vetting transients
- Multichannel OME-Zarr and OME-TIFF: channel contrast, z-slices, time points
- Draw regions or click cells to classify them, export GeoJSON that QuPath reads
- FITS cutouts with science/reference/difference triplets for vetting transients
Easy to use, even if you have never coded:
• runs in a Jupyter notebook
• fill in one form, click Submit, run one more cell
• one file or a whole folder (batch mode)
• reads .czi, .tif and OME-TIFF
• runs in a Jupyter notebook
• fill in one form, click Submit, run one more cell
• one file or a whole folder (batch mode)
• reads .czi, .tif and OME-TIFF
October 29, 2026 at 9:54 AM
Easy to use, even if you have never coded:
• runs in a Jupyter notebook
• fill in one form, click Submit, run one more cell
• one file or a whole folder (batch mode)
• reads .czi, .tif and OME-TIFF
• runs in a Jupyter notebook
• fill in one form, click Submit, run one more cell
• one file or a whole folder (batch mode)
• reads .czi, .tif and OME-TIFF
And two command line tools in every package, no code required:
slideio-converter — convert a slide or a region into tiled pyramidal
OME-TIFF or SVS
slideio-tiffinspector — dump a TIFF's directory structure
slideio.com/tools.html
slideio-converter — convert a slide or a region into tiled pyramidal
OME-TIFF or SVS
slideio-tiffinspector — dump a TIFF's directory structure
slideio.com/tools.html
Tools · SlideIO
slideio.com
October 4, 2026 at 1:35 PM
And two command line tools in every package, no code required:
slideio-converter — convert a slide or a region into tiled pyramidal
OME-TIFF or SVS
slideio-tiffinspector — dump a TIFF's directory structure
slideio.com/tools.html
slideio-converter — convert a slide or a region into tiled pyramidal
OME-TIFF or SVS
slideio-tiffinspector — dump a TIFF's directory structure
slideio.com/tools.html
SlideIO 2.10.0 is out — the open-source library for reading whole-slide images from Python and C++. 12 formats: SVS, NDPI, CZI, DICOM WSI, OME-TIFF, Philips TIFF and more.
pip install slideio
slideio.com
pip install slideio
slideio.com
SlideIO
slideio.com
October 4, 2026 at 1:35 PM
SlideIO 2.10.0 is out — the open-source library for reading whole-slide images from Python and C++. 12 formats: SVS, NDPI, CZI, DICOM WSI, OME-TIFF, Philips TIFF and more.
pip install slideio
slideio.com
pip install slideio
slideio.com
🚀 #MotilA now runs with #OMIO!
v1.1.2 adds much more flexible image I/O: #TIFF/ #OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO & normalized to TZCYX axis-order, automatically. No more manual axis reordering before analysis🤗
🌍 motila.readthedocs.io/en/latest/ch...
#microglia #motility
v1.1.2 adds much more flexible image I/O: #TIFF/ #OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO & normalized to TZCYX axis-order, automatically. No more manual axis reordering before analysis🤗
🌍 motila.readthedocs.io/en/latest/ch...
#microglia #motility
August 11, 2026 at 3:07 PM
🚀 #MotilA now runs with #OMIO!
v1.1.2 adds much more flexible image I/O: #TIFF/ #OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO & normalized to TZCYX axis-order, automatically. No more manual axis reordering before analysis🤗
🌍 motila.readthedocs.io/en/latest/ch...
#microglia #motility
v1.1.2 adds much more flexible image I/O: #TIFF/ #OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO & normalized to TZCYX axis-order, automatically. No more manual axis reordering before analysis🤗
🌍 motila.readthedocs.io/en/latest/ch...
#microglia #motility
Yey, I figured out how to display 3D movie stacks in #ChimeraX, thanks to @dabiophysicist.bsky.social for the suggestion. My original tiff was not ome-tiff so you'll need to convert it first (do this with #Python), then adjust voxelsize in ChimeraX so the image isn't flat, record, and voila!
July 27, 2026 at 5:14 PM
Yey, I figured out how to display 3D movie stacks in #ChimeraX, thanks to @dabiophysicist.bsky.social for the suggestion. My original tiff was not ome-tiff so you'll need to convert it first (do this with #Python), then adjust voxelsize in ChimeraX so the image isn't flat, record, and voila!
File formats of biology-relevant images:
During acquisition: use the default file format for your microscope and acquisition software.
During analysis: use the default file format for the analysis software you’re using – or OME-TIFF.
bioimagebook.github.io/chapters/1-c...
During acquisition: use the default file format for your microscope and acquisition software.
During analysis: use the default file format for the analysis software you’re using – or OME-TIFF.
bioimagebook.github.io/chapters/1-c...
Files & file formats — Introduction to Bioimage Analysis
bioimagebook.github.io
December 23, 2025 at 11:26 AM
File formats of biology-relevant images:
During acquisition: use the default file format for your microscope and acquisition software.
During analysis: use the default file format for the analysis software you’re using – or OME-TIFF.
bioimagebook.github.io/chapters/1-c...
During acquisition: use the default file format for your microscope and acquisition software.
During analysis: use the default file format for the analysis software you’re using – or OME-TIFF.
bioimagebook.github.io/chapters/1-c...
TIFF vs. OME-TIFF
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
September 1, 2025 at 12:24 PM
TIFF vs. OME-TIFF
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
#OME is now verified on @bsky.app! Follow to find out more about #Bio-Formats, #OMERO, #OME-TIFF, #OME-Zarr, #IDR, and much, much more.
openmicroscopy.org
openmicroscopy.org
The Open Microscopy Environment
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
openmicroscopy.org
December 3, 2024 at 11:45 AM
#OME is now verified on @bsky.app! Follow to find out more about #Bio-Formats, #OMERO, #OME-TIFF, #OME-Zarr, #IDR, and much, much more.
openmicroscopy.org
openmicroscopy.org
I think that's what ilastik's main user base needs. Now our no-code users can seamlessly go from tiff, to h5, to ome-zarr, whichever best suits their machine.
November 11, 2025 at 11:15 AM
I think that's what ilastik's main user base needs. Now our no-code users can seamlessly go from tiff, to h5, to ome-zarr, whichever best suits their machine.
RAWtunda: a Tool to Convert a Multi-Channel Raw Image into TIFF and OME-TIFF Formats https://www.biorxiv.org/content/10.1101/2025.10.25.684557v1
October 30, 2025 at 11:47 AM
RAWtunda: a Tool to Convert a Multi-Channel Raw Image into TIFF and OME-TIFF Formats https://www.biorxiv.org/content/10.1101/2025.10.25.684557v1
Vitessce
Integrative visualization of multimodal & spatially resolved single-cell data
vitessce.io
Python/R/Java/online configuration editor
Support multiple data types/file formats
SpatialData AnnData MuData CSV OME-TIFF OME-Zarr
@naturemethods.bsky.social 2025
www.nature.com/articles/s41...
Integrative visualization of multimodal & spatially resolved single-cell data
vitessce.io
Python/R/Java/online configuration editor
Support multiple data types/file formats
SpatialData AnnData MuData CSV OME-TIFF OME-Zarr
@naturemethods.bsky.social 2025
www.nature.com/articles/s41...
April 15, 2025 at 11:28 AM
Vitessce
Integrative visualization of multimodal & spatially resolved single-cell data
vitessce.io
Python/R/Java/online configuration editor
Support multiple data types/file formats
SpatialData AnnData MuData CSV OME-TIFF OME-Zarr
@naturemethods.bsky.social 2025
www.nature.com/articles/s41...
Integrative visualization of multimodal & spatially resolved single-cell data
vitessce.io
Python/R/Java/online configuration editor
Support multiple data types/file formats
SpatialData AnnData MuData CSV OME-TIFF OME-Zarr
@naturemethods.bsky.social 2025
www.nature.com/articles/s41...
🐧 **OMERewriter – edit common fields in OME-TIFF files**
OMERewriter is a desktop application for microscopy imaging workflows that focuses on working with OME-TIFF metadata. The post OMERewriter – edit common fields in OME-TIFF files appeared first on L...
📰 Source: LinuxLinks
🔗 Link […]
OMERewriter is a desktop application for microscopy imaging workflows that focuses on working with OME-TIFF metadata. The post OMERewriter – edit common fields in OME-TIFF files appeared first on L...
📰 Source: LinuxLinks
🔗 Link […]
Original post on igeek.gamer-geek-news.com
igeek.gamer-geek-news.com
April 23, 2026 at 10:28 PM
🐧 **OMERewriter – edit common fields in OME-TIFF files**
OMERewriter is a desktop application for microscopy imaging workflows that focuses on working with OME-TIFF metadata. The post OMERewriter – edit common fields in OME-TIFF files appeared first on L...
📰 Source: LinuxLinks
🔗 Link […]
OMERewriter is a desktop application for microscopy imaging workflows that focuses on working with OME-TIFF metadata. The post OMERewriter – edit common fields in OME-TIFF files appeared first on L...
📰 Source: LinuxLinks
🔗 Link […]
🐧 **OMERewriter – view and rewrite OME-TIFF metadata**
OMERewriter is a desktop application for working with microscopy image metadata stored in OME-TIFF files. The post OMERewriter – view and rewrite OME-TIFF metadata appeared first on LinuxLinks.
📰 Source: LinuxLinks
🔗 Link […]
OMERewriter is a desktop application for working with microscopy image metadata stored in OME-TIFF files. The post OMERewriter – view and rewrite OME-TIFF metadata appeared first on LinuxLinks.
📰 Source: LinuxLinks
🔗 Link […]
Original post on igeek.gamer-geek-news.com
igeek.gamer-geek-news.com
April 13, 2026 at 7:06 PM
🐧 **OMERewriter – view and rewrite OME-TIFF metadata**
OMERewriter is a desktop application for working with microscopy image metadata stored in OME-TIFF files. The post OMERewriter – view and rewrite OME-TIFF metadata appeared first on LinuxLinks.
📰 Source: LinuxLinks
🔗 Link […]
OMERewriter is a desktop application for working with microscopy image metadata stored in OME-TIFF files. The post OMERewriter – view and rewrite OME-TIFF metadata appeared first on LinuxLinks.
📰 Source: LinuxLinks
🔗 Link […]
Here's where the documentation says 3D tiff stacks should work, and 4D-series.ome.tif (docs.openmicroscopy.org/ome-model/5....) opens as a veries. The key seems to be ImageJ metadata, try bfconvert in.tif out.tif.
July 24, 2026 at 7:01 PM
Here's where the documentation says 3D tiff stacks should work, and 4D-series.ome.tif (docs.openmicroscopy.org/ome-model/5....) opens as a veries. The key seems to be ImageJ metadata, try bfconvert in.tif out.tif.
Crazy idea that might actually be not-too-hard to implement: a FUSE file system that exposes all images as a OME-TIFF supported file, then performs on-the-fly conversion from JEPG-XL lossless
It’s been done with MP3 files before (yacufs)
It’s been done with MP3 files before (yacufs)
November 8, 2024 at 10:21 PM
Crazy idea that might actually be not-too-hard to implement: a FUSE file system that exposes all images as a OME-TIFF supported file, then performs on-the-fly conversion from JEPG-XL lossless
It’s been done with MP3 files before (yacufs)
It’s been done with MP3 files before (yacufs)
Dworak et al. RAWtunda: a Tool to Convert a Multi-Channel Raw Image into TIFF and OME-TIFF Formats
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 26, 2025 at 3:07 PM
Dworak et al. RAWtunda: a Tool to Convert a Multi-Channel Raw Image into TIFF and OME-TIFF Formats
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Slower acquisition than the Echo Revolution. Also the Analyzer software is terrible whereas the Revolution automatically computes the EDF on the fly and just generates a stitched image at the for direct OME TIFF output. I hate the Analyzer software. It is completely non-intuitive.
March 7, 2026 at 6:51 PM
Slower acquisition than the Echo Revolution. Also the Analyzer software is terrible whereas the Revolution automatically computes the EDF on the fly and just generates a stitched image at the for direct OME TIFF output. I hate the Analyzer software. It is completely non-intuitive.
Today’s release of #OMIO v0.2.6 is again a small update, but 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/ch...
🌍 omio.readthedocs.io/en/latest/ch...
July 29, 2026 at 9:55 PM
Today’s release of #OMIO v0.2.6 is again a small update, but 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/ch...
🌍 omio.readthedocs.io/en/latest/ch...
#OMIO currently supports: #TIFF, #OMETIFF, #TIFFseries, #ZEISS #LSM and #CZI, #Thorlabs' RAW format. All inputs are mapped to a unified representation with #OME-compatible axis semantics and standardized metadata handling.
🧵2/N
🧵2/N
June 12, 2026 at 3:23 PM
#OMIO currently supports: #TIFF, #OMETIFF, #TIFFseries, #ZEISS #LSM and #CZI, #Thorlabs' RAW format. All inputs are mapped to a unified representation with #OME-compatible axis semantics and standardized metadata handling.
🧵2/N
🧵2/N
RAWtunda: a Tool to Convert a Multi-Channel Raw Image into TIFF and OME-TIFF Formats https://www.biorxiv.org/content/10.1101/2025.10.25.684557v1
October 30, 2025 at 11:47 AM
RAWtunda: a Tool to Convert a Multi-Channel Raw Image into TIFF and OME-TIFF Formats https://www.biorxiv.org/content/10.1101/2025.10.25.684557v1
#microscopycommunity- do you use BioFormats, OMERO, OME-TIFF, OME-Zarr or are you interested in open source and microscopy? Then you should check out the recordings from OME2025!
buff.ly/fgUxoQf
@openmicroscopy.org
@gerbi-gmb.de.
@jacksonlab.bsky.social
@mblscience.bsky.social
buff.ly/fgUxoQf
@openmicroscopy.org
@gerbi-gmb.de.
@jacksonlab.bsky.social
@mblscience.bsky.social
June 18, 2025 at 6:47 PM
#microscopycommunity- do you use BioFormats, OMERO, OME-TIFF, OME-Zarr or are you interested in open source and microscopy? Then you should check out the recordings from OME2025!
buff.ly/fgUxoQf
@openmicroscopy.org
@gerbi-gmb.de.
@jacksonlab.bsky.social
@mblscience.bsky.social
buff.ly/fgUxoQf
@openmicroscopy.org
@gerbi-gmb.de.
@jacksonlab.bsky.social
@mblscience.bsky.social