#image-analysis — Public Fediverse posts

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

We are happy to announce the "NL-BioImaging Advanced Image Analysis course for biologists", 21–24 September at Erasmus MC in Rotterdam.

More info and register here:
https://courses.microscopie.nl/?event_id=527

Four hands-on days going from segmentation to full pipelines:
- Automate reproducible image processing with Jupyter notebooks
- Assess classical and AI approaches for specific challenges
- Train and optimise deep learning models on biological datasets
- Document and publish reproducible image analysis pipelines

Guidance from experts across the Netherlands.
Limited to 20 participants.

Feel free to tag colleagues or share this with your network!

#bioimaging #imageanalysis #course #openscience
#cellpose #OMERO #Jupyter #napari #FAIRdata
NL-Bioimaging #NVvM

I didn't realise that Gabriel Landini - who contributed many scripts and tools to ImageJ - died last year. There's a little tribute to him here.

https://forum.image.sc/t/unable-to-download-local-threshold-plugin/121491/4

#ImageAnalysis #Microscopy #CellBiology

I didn't realise that Gabriel Landini - who contributed many scripts and tools to ImageJ - died last year. There's a little tribute to him here.

https://forum.image.sc/t/unable-to-download-local-threshold-plugin/121491/4

#ImageAnalysis #Microscopy #CellBiology

Very interesting study with alarming results. And we're not talking about the LLM's from big tech, but tools that are regarded as a useful deployment of pattern recognition systems.
Maybe still very useful, but we have think very carefully about the way we deploy them.
#AI #dataanalysis #patternrecognition #imageanalysis #healthcare
https://www.nature.com/articles/d41586-026-01947-1

Very interesting study with alarming results. And we're not talking about the LLM's from big tech, but tools that are regarded as a useful deployment of pattern recognition systems.
Maybe still very useful, but we have think very carefully about the way we deploy them.
#AI #dataanalysis #patternrecognition #imageanalysis #healthcare
https://www.nature.com/articles/d41586-026-01947-1

Job alerts! Senior Image Data Scientist (x2!) and Senior Scientific Software Developer - Bioimage Informatics at the Center for Bioimage Informatics at St Jude Children's Research Hospital. These seem pretty nice.

https://forum.image.sc/t/opportunities-st-jude-childrens-research-hospital/121557

#GetFediHired #ImageAnalysis #Imaging

Job alerts! Senior Image Data Scientist (x2!) and Senior Scientific Software Developer - Bioimage Informatics at the Center for Bioimage Informatics at St Jude Children's Research Hospital. These seem pretty nice.

https://forum.image.sc/t/opportunities-st-jude-childrens-research-hospital/121557

#GetFediHired #ImageAnalysis #Imaging

Pipeline release! nf-core/lsmquant v1.0.2 - 1.0.2 - Excited Squid !
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.2

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.2 - 1.0.2 - Excited Squid !
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.2

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

@helenajambor Preibisch's "new Lenna" is legendary in #ImageAnalysis circles!

@helenajambor Preibisch's "new Lenna" is legendary in #ImageAnalysis circles!

I have been building a smart water bowl to measure pet water consumption. Scale + camera + raspberry pi. I'm at the image recognition part of training a neural net to identify the pet involved (we have 2 black labs, 1 black cat and 2 tuxedos) and it's harder than you'd think... #imageAnalysis #catsofMastodon #dogsofmastodon

I have been building a smart water bowl to measure pet water consumption. Scale + camera + raspberry pi. I'm at the image recognition part of training a neural net to identify the pet involved (we have 2 black labs, 1 black cat and 2 tuxedos) and it's harder than you'd think... #imageAnalysis #catsofMastodon #dogsofmastodon

Pipeline release! nf-core/lsmquant v1.0.1 - Excited Squid Patch!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.1

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.1 - Excited Squid Patch!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.1

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

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

Registration is open!

Want to better validate your #AI methods in #imageanalysis?

Join our 3-part online workshop on June 3, 9 & 25 at 9-12 PM.

Learn to choose metrics, quantify uncertainty & assess the robustness of rankings.

⏳ Register by May 31 👉 https://bit.ly/Validating-AI-for-Image-Analysis

#imaging #training

@association @helmholtz_hmc

Registration is open!

Want to better validate your #AI methods in #imageanalysis?

Join our 3-part online workshop on June 3, 9 & 25 at 9-12 PM.

Learn to choose metrics, quantify uncertainty & assess the robustness of rankings.

⏳ Register by May 31 👉 https://bit.ly/Validating-AI-for-Image-Analysis

#imaging #training

@association @helmholtz_hmc

Doing #AI for #imageanalysis? Learn how to validate your results properly:

1️⃣Select appropriate performance metrics
2️⃣Quantify model performance uncertainty
3️⃣Assess the robustness of model comparisons

🗓️ June 3 | 9 | 25, 9-12

Registration opens May 6 👉 https://bit.ly/Validating-AI-for-Image-Analysis

Instructors: Annika Reinke, Helmholtz Imaging, DKFZ & Evangelia Christodoulou, DKFZ

This course is organized in cooperation with HIDA.

#imaging #training @association

Doing #AI for #imageanalysis? Learn how to validate your results properly:

1️⃣Select appropriate performance metrics
2️⃣Quantify model performance uncertainty
3️⃣Assess the robustness of model comparisons

🗓️ June 3 | 9 | 25, 9-12

Registration opens May 6 👉 https://bit.ly/Validating-AI-for-Image-Analysis

Instructors: Annika Reinke, Helmholtz Imaging, DKFZ & Evangelia Christodoulou, DKFZ

This course is organized in cooperation with HIDA.

#imaging #training @association

Pipeline release! nf-core/lsmquant v1.0.0 - 1.0.0 - Excited Squid!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.0

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.0 - 1.0.0 - Excited Squid!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.0

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.0 - 1.0.0 - Excited Squid!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.0

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.0 - 1.0.0 - Excited Squid!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.0

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

How Do You Find an Illegal Image Without Looking at It?

https://mahmoud-salem.net/the-invisible-shield

#HackerNews #illegalcontent #digitalprivacy #imageanalysis #cybersecurity

How Do You Find an Illegal Image Without Looking at It?

https://mahmoud-salem.net/the-invisible-shield

#HackerNews #illegalcontent #digitalprivacy #imageanalysis #cybersecurity

The image in question is not outdated. A thorough comparison of distance, edges, sky, and surrounding walls confirms its relevance. #ImageAnalysis #OSINT

🔬 Registration is open for our pilot Introduction to napari Workshop!

napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.

✅ Only $20 USD
✅ Limited to 20 people
✅ Perfect for biologists, imaging specialists & data scientists

Two workshops at two different times.

#napari #Python #ImageAnalysis #DataScience #OpenSource

🔬 Registration is open for our pilot Introduction to napari Workshop!

napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.

✅ Only $20 USD
✅ Limited to 20 people
✅ Perfect for biologists, imaging specialists & data scientists

Two workshops at two different times.

#napari #Python #ImageAnalysis #DataScience #OpenSource

Drivers Of Forest Disturbance In Southeast Asia [incl. spatial analysis]
--
https://doi.org/10.1016/j.jag.2026.105220 <-- shared paper 🔗
--
https://github.com/shijuanchen/SEA_forest_dis <-- shared GitHub ‘data repository 🔗
--
#GIS #spatial #mapping #spatialanalysis #spatiotemporal #forest #vegetation #Forestdisturbance #Forestdegradation #Deforestation #remotesensing #SoutheastAsia #Asia #tropicalforests #timeseriesanalysis #geostatistics #disturbance #clearing #planting #agriculture #earthobservation #imagery #CCDC #changedetection #landcover #landuse #change #plantation #cultivation #slashandburn #planning #mitigation #catalogue #conservation #management #landmanagement #machinelearning #imageanalysis #AI

Drivers Of Forest Disturbance In Southeast Asia [incl. spatial analysis]
--
https://doi.org/10.1016/j.jag.2026.105220 <-- shared paper 🔗
--
https://github.com/shijuanchen/SEA_forest_dis <-- shared GitHub ‘data repository 🔗
--
#GIS #spatial #mapping #spatialanalysis #spatiotemporal #forest #vegetation #Forestdisturbance #Forestdegradation #Deforestation #remotesensing #SoutheastAsia #Asia #tropicalforests #timeseriesanalysis #geostatistics #disturbance #clearing #planting #agriculture #earthobservation #imagery #CCDC #changedetection #landcover #landuse #change #plantation #cultivation #slashandburn #planning #mitigation #catalogue #conservation #management #landmanagement #machinelearning #imageanalysis #AI

What would you align sets of multiple (~20) large (2-4 Gb) #microscopy images?

For smaller subset images ImageJ plugins for transformations based on SIFT landmark correspondence work well. However standard ImageJ (bioformats) file handling doesn’t cope well with such large files. For plugins handling large file manipulation (BigData family) or chunked (e.g. zarr) storage in turn I don’t know how to implement SIFT (or similar) - e.g. for BigWarp I can only find manual landmark annotation, i.e. no option to create landmarks via other plugins.

My images are iterative fluorescence whole slide scans of the same slide with a constant nuclear stain and varying other stains. There is some x/y shift and rotation as well as warping - nothing major, but I need nearly pixel perfect alignment (e.g. QuPath+Warpy worked well on larger images but was too imprecise).
Stitching happens on the fly during imaging and I’m not sure I can extract the tiles faithfully, so the ASHLAR pipeline didn’t seem applicable. I’ve seen VALIS recommended, but implementation seemed daunting and since the nuclear stain provides reasonable fiducial points the workflow seemed an overkill.

Ideally I would want a scripted solution as this has to scale up to hundreds of such sets eventually and downstream processing is in python+R anyhow.

#imageanalysis #spatial #imaging

What would you align sets of multiple (~20) large (2-4 Gb) #microscopy images?

For smaller subset images ImageJ plugins for transformations based on SIFT landmark correspondence work well. However standard ImageJ (bioformats) file handling doesn’t cope well with such large files. For plugins handling large file manipulation (BigData family) or chunked (e.g. zarr) storage in turn I don’t know how to implement SIFT (or similar) - e.g. for BigWarp I can only find manual landmark annotation, i.e. no option to create landmarks via other plugins.

My images are iterative fluorescence whole slide scans of the same slide with a constant nuclear stain and varying other stains. There is some x/y shift and rotation as well as warping - nothing major, but I need nearly pixel perfect alignment (e.g. QuPath+Warpy worked well on larger images but was too imprecise).
Stitching happens on the fly during imaging and I’m not sure I can extract the tiles faithfully, so the ASHLAR pipeline didn’t seem applicable. I’ve seen VALIS recommended, but implementation seemed daunting and since the nuclear stain provides reasonable fiducial points the workflow seemed an overkill.

Ideally I would want a scripted solution as this has to scale up to hundreds of such sets eventually and downstream processing is in python+R anyhow.

#imageanalysis #spatial #imaging

@simon_brooke

Eerie… but then again context is everything. Google has access to a huge amount of information in the images and exif information if available. Correlating all of this across its huge user base provides possibilities we cannot even imagine.

These companies and their tools already know more of us than we know about ourselves. We are the product.

Ever realized why we need rules and regulations around privacy?

#ai #privacy #google #ImageAnalysis

@simon_brooke

Eerie… but then again context is everything. Google has access to a huge amount of information in the images and exif information if available. Correlating all of this across its huge user base provides possibilities we cannot even imagine.

These companies and their tools already know more of us than we know about ourselves. We are the product.

Ever realized why we need rules and regulations around privacy?

#ai #privacy #google #ImageAnalysis

I have two open positions in my lab at the Advanced Light Microscopy Unit Centre for Genomic Regulation (CRG):

- Imaging Scientist (permanent position. Deadline 11th Nov.) https://recruitment.crg.eu/content/jobs/position/imaging-scientists-advanced-light-microscopy-unit-almu

- Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) https://recruitment.crg.eu/content/jobs/position/entry-level-imaging-scientist-advanced-light-microscopy-unit-almu

If you have any questions don’t hesitate to reach out.

Boosts appreciated.

#getfedihired #fedihire #jobSearch #jobposting #Microscopy #Optics #ImageAnalysis

I have two open positions in my lab at the Advanced Light Microscopy Unit Centre for Genomic Regulation (CRG):

- Imaging Scientist (permanent position. Deadline 11th Nov.) https://recruitment.crg.eu/content/jobs/position/imaging-scientists-advanced-light-microscopy-unit-almu

- Entry-Level Imaging Scientist (12 months fixed-term position. Deadline 18th Nov.) https://recruitment.crg.eu/content/jobs/position/entry-level-imaging-scientist-advanced-light-microscopy-unit-almu

If you have any questions don’t hesitate to reach out.

Boosts appreciated.

#getfedihired #fedihire #jobSearch #jobposting #Microscopy #Optics #ImageAnalysis

Position open: Head of the Center for Microscopy and Image Analysis (Core Facility) at the Center for Microscopy and Image Analysis (ZMB) in the University of Zurich, Switzerland.

https://www.nature.com/naturecareers/job/12847076/head-of-the-center-for-microscopy-and-image-analysis-core-facility-/

#microscopy #PhDJobs #academia #ElectronMicroscopy #LightMicroscopy #ImageAnalysis

Position open: Head of the Center for Microscopy and Image Analysis (Core Facility) at the Center for Microscopy and Image Analysis (ZMB) in the University of Zurich, Switzerland.

https://www.nature.com/naturecareers/job/12847076/head-of-the-center-for-microscopy-and-image-analysis-core-facility-/

#microscopy #PhDJobs #academia #ElectronMicroscopy #LightMicroscopy #ImageAnalysis

Last week to subscribe for our FREE Webinar Series on "Mastering Colocalization Analysis"; from raw image to scientific results in minutes. Reserve your seat now!
http://svi.nl/webinarinvitation
#imaging #microscopy #cellbiology #fluorescence #imageanalysis #colocalization

Today our team member Anna Breger tells her story - “Many little twists and turns have brought me to where I am now and I am absolutely thrilled about my interdisciplinary research project working on image analysis and historical music manuscripts.”

➡️ Find her full story at https://hermathsstory.eu/anna-breger/

#AppliedMathematics #ImageAnalysis #Music #InterdisciplinaryResearch #NonTraditionalPathways #DataScience #HerMathsStory

Today our team member Anna Breger tells her story - “Many little twists and turns have brought me to where I am now and I am absolutely thrilled about my interdisciplinary research project working on image analysis and historical music manuscripts.”

➡️ Find her full story at https://hermathsstory.eu/anna-breger/

#AppliedMathematics #ImageAnalysis #Music #InterdisciplinaryResearch #NonTraditionalPathways #DataScience #HerMathsStory

New tutorial from the Galaxy Training Network! Learn how to quantify gel electrophoresis bands using QuPath + Galaxy. Fully open, reproducible, and beginner-friendly.
https://training.galaxyproject.org/training-material/news/2025/08/18/bands_image_analysis.html

@galaxyfreiburg
#Bioinformatics #ImageAnalysis #GelElectrophoresis #OpenScience #ReproducibleResearch #GalaxyProject #QuPath #Bioimaging #LifeSciences #OpenSourceTools #ScienceEducation #DataAnalysis #ResearchTools

New tutorial from the Galaxy Training Network! Learn how to quantify gel electrophoresis bands using QuPath + Galaxy. Fully open, reproducible, and beginner-friendly.
https://training.galaxyproject.org/training-material/news/2025/08/18/bands_image_analysis.html

@galaxyfreiburg
#Bioinformatics #ImageAnalysis #GelElectrophoresis #OpenScience #ReproducibleResearch #GalaxyProject #QuPath #Bioimaging #LifeSciences #OpenSourceTools #ScienceEducation #DataAnalysis #ResearchTools

New tutorial from the Galaxy Training Network! Learn how to quantify gel electrophoresis bands using QuPath + Galaxy. Fully open, reproducible, and beginner-friendly.
https://training.galaxyproject.org/training-material/news/2025/08/18/bands_image_analysis.html

@galaxyproject
#Bioinformatics #ImageAnalysis #GelElectrophoresis #OpenScience #ReproducibleResearch #GalaxyProject #QuPath #Bioimaging #LifeSciences #OpenSourceTools #ScienceEducation #DataAnalysis #ResearchTools

New tutorial from the Galaxy Training Network! Learn how to quantify gel electrophoresis bands using QuPath + Galaxy. Fully open, reproducible, and beginner-friendly.
https://training.galaxyproject.org/training-material/news/2025/08/18/bands_image_analysis.html

@galaxyproject
#Bioinformatics #ImageAnalysis #GelElectrophoresis #OpenScience #ReproducibleResearch #GalaxyProject #QuPath #Bioimaging #LifeSciences #OpenSourceTools #ScienceEducation #DataAnalysis #ResearchTools

version 0.7-0 of my R package `bayesImageS' is now available on CRAN for Linux and macOS
(Windows binaries are still being built and should be available soon)

The main change is a reduction in the console output for the exchange algorithm. There were also some minor changes to fix WARN and NOTE due to compatibility issues with the latest RcppArmadillo, which now uses the
Armadillo 15 linear algebra library by default.

https://cran.r-project.org/package=bayesImageS

#rstats #bayesian #ImageAnalysis

Transformer-Ensemble-Based Implicit Spectral–Spatial Functions for Arbitrary-Resolution Hyperspectral Pansharpening.
IEEE Transactions on Geoscience and Remote Sensing, vol. 63, pp. 1-19, 2025, Art no. 5519519
https://doi.org/10.1109/TGRS.2025.3589021
#ai #transformers #imageanalysis
bsky https://bsky.app/profile/clirspec.org

Sept 25: Learn to track objects over time and instances. With Carsten Rother (@uniheidelberg).

Register for the series 👉 https://bit.ly/6-image-processing-tasks

@helmholtz
#imaging #Tracking #ImageAnalysis

👏 Big congrats to Annika Reinke for winning the Hector Foundation Prize 2025 for Metrics Reloaded, setting new standards for AI in image analysis.

Learn more, explore the tool & meet all awardees in a video 👉 https://helmholtz-imaging.de/news/hector-foundation-prize-for-annika-reinke/

#helmholtz #helmholtzimaging #imaging #metrics #metricsreloaded #AI #imageanalysis

@association @DKFZ