#image-analysis — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #image-analysis, aggregated by home.social.
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People doing #microscopy #ImageAnalysis , would you recommend a graphics tablet working with linux (and ideally #napari) to help fix image segmentation?
To better explain my problem, I am working with images of bacteria (first image). I am developing software that segments them (second image). But sometimes the segmentation is poor and I need to fix it by hand (third image). Doing it with a mouse is not great, so I thought that a graphics tablet might help.
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People doing #microscopy #ImageAnalysis , would you recommend a graphics tablet working with linux (and ideally #napari) to help fix image segmentation?
To better explain my problem, I am working with images of bacteria (first image). I am developing software that segments them (second image). But sometimes the segmentation is poor and I need to fix it by hand (third image). Doing it with a mouse is not great, so I thought that a graphics tablet might help.
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People doing #microscopy #ImageAnalysis , would you recommend a graphics tablet working with linux (and ideally #napari) to help fix image segmentation?
To better explain my problem, I am working with images of bacteria (first image). I am developing software that segments them (second image). But sometimes the segmentation is poor and I need to fix it by hand (third image). Doing it with a mouse is not great, so I thought that a graphics tablet might help.
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People doing #microscopy #ImageAnalysis , would you recommend a graphics tablet working with linux (and ideally #napari) to help fix image segmentation?
To better explain my problem, I am working with images of bacteria (first image). I am developing software that segments them (second image). But sometimes the segmentation is poor and I need to fix it by hand (third image). Doing it with a mouse is not great, so I thought that a graphics tablet might help.
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The first NL-BioImaging Advanced Image Analysis Course is almost coming to an end.
Over the past few days we have covered a lot of topics: the Python ecosystem for image analysis, OMERO, AI segmentation and training, and hands-on deep learning with BiaPy for bioimage segmentation.
Everyone worked hard during the data challenge to get the most out of their data.A huge thanks to all the trainers from across the Dutch bioimaging community: LUMC, Amsterdam UMC, UMCG, UM, UvA, NKI, UU. A special thanks to Joel Lüthi and Daniel Franco Barranco, for joining us online.
Like to learn more? The training materials can be found here:
https://nl-bioimaging.github.io/NL-BioImageAnalysis-course2026/
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The first NL-BioImaging Advanced Image Analysis Course is almost coming to an end.
Over the past few days we have covered a lot of topics: the Python ecosystem for image analysis, OMERO, AI segmentation and training, and hands-on deep learning with BiaPy for bioimage segmentation.
Everyone worked hard during the data challenge to get the most out of their data.A huge thanks to all the trainers from across the Dutch bioimaging community: LUMC, Amsterdam UMC, UMCG, UM, UvA, NKI, UU. A special thanks to Joel Lüthi and Daniel Franco Barranco, for joining us online.
Like to learn more? The training materials can be found here:
https://nl-bioimaging.github.io/NL-BioImageAnalysis-course2026/
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Registration open now: Image Dataset Quality Control, Data Exploration & Pixel Patrol
Learn to spot dataset issues, visualize metadata & prepare image collections for analysis.
📅 Sept 10+17, 2026
💻 OnlineRegister here 👉 https://events.hifis.net/event/3675/
Free for @association & @hidadigital partners.
#imaging #imagingscience #helmholtz #training #imagequality #imageanalysis
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Registration open now: Image Dataset Quality Control, Data Exploration & Pixel Patrol
Learn to spot dataset issues, visualize metadata & prepare image collections for analysis.
📅 Sept 10+17, 2026
💻 OnlineRegister here 👉 https://events.hifis.net/event/3675/
Free for @association & @hidadigital partners.
#imaging #imagingscience #helmholtz #training #imagequality #imageanalysis
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Registration open now: Image Dataset Quality Control, Data Exploration & Pixel Patrol
Learn to spot dataset issues, visualize metadata & prepare image collections for analysis.
📅 Sept 10+17, 2026
💻 OnlineRegister here 👉 https://events.hifis.net/event/3675/
Free for @association & @hidadigital partners.
#imaging #imagingscience #helmholtz #training #imagequality #imageanalysis
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Registration open now: Image Dataset Quality Control, Data Exploration & Pixel Patrol
Learn to spot dataset issues, visualize metadata & prepare image collections for analysis.
📅 Sept 10+17, 2026
💻 OnlineRegister here 👉 https://events.hifis.net/event/3675/
Free for @association & @hidadigital partners.
#imaging #imagingscience #helmholtz #training #imagequality #imageanalysis
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Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - 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/1.0.3#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - 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/1.0.3#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - 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/1.0.3#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - 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/1.0.3#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics
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Do you already have cleared-brain image stacks, but don't know what to do with them? Or maybe you want to learn which parameters are important before embarking on an imaging campaign? In this intensive 2-day hands-on workshop you will learn how to handle 3D #lightsheetmicroscopy data, how to work with the DELiVR pipeline, and how to create your own annotations in #VR.
September 9-10th, at the Ertürk lab at @HelmholtzMunich in Munich, Germany.
(1/2)
#neuroscience #tissueclearing #imageanalysis -
Do you already have cleared-brain image stacks, but don't know what to do with them? Or maybe you want to learn which parameters are important before embarking on an imaging campaign? In this intensive 2-day hands-on workshop you will learn how to handle 3D #lightsheetmicroscopy data, how to work with the DELiVR pipeline, and how to create your own annotations in #VR.
September 9-10th, at the Ertürk lab at @HelmholtzMunich in Munich, Germany.
(1/2)
#neuroscience #tissueclearing #imageanalysis -
Do you already have cleared-brain image stacks, but don't know what to do with them? Or maybe you want to learn which parameters are important before embarking on an imaging campaign? In this intensive 2-day hands-on workshop you will learn how to handle 3D #lightsheetmicroscopy data, how to work with the DELiVR pipeline, and how to create your own annotations in #VR.
September 9-10th, at the Ertürk lab at @HelmholtzMunich in Munich, Germany.
(1/2)
#neuroscience #tissueclearing #imageanalysis -
Do you already have cleared-brain image stacks, but don't know what to do with them? Or maybe you want to learn which parameters are important before embarking on an imaging campaign? In this intensive 2-day hands-on workshop you will learn how to handle 3D #lightsheetmicroscopy data, how to work with the DELiVR pipeline, and how to create your own annotations in #VR.
September 9-10th, at the Ertürk lab at @HelmholtzMunich in Munich, Germany.
(1/2)
#neuroscience #tissueclearing #imageanalysis -
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
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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
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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
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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
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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
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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
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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
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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
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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=527Four 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 pipelinesGuidance 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 -
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=527Four 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 pipelinesGuidance 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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@helenajambor Preibisch's "new Lenna" is legendary in #ImageAnalysis circles!
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@helenajambor Preibisch's "new Lenna" is legendary in #ImageAnalysis circles!
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@helenajambor Preibisch's "new Lenna" is legendary in #ImageAnalysis circles!
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@helenajambor Preibisch's "new Lenna" is legendary in #ImageAnalysis circles!
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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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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
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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