Judith Garcia-Gonzalez
@garciagj.bsky.social
Bioimage analyst in the making 🔬| Plant biologist 🌱 | Geneticist 🧬
VMCF @ Charles university | Imaging Facility @ Institute of Experimental Botany of the Czech Academy of Sciences
🇪🇸🇨🇿
VMCF @ Charles university | Imaging Facility @ Institute of Experimental Botany of the Czech Academy of Sciences
🇪🇸🇨🇿
Reposted by Judith Garcia-Gonzalez
AI has so much potential for interpreting biological images, and yet, annotated biological datasets needed to train AI tools remain scarce.
If you generate microscopy data or develop AI tools to interpret it, check it these new guidelines:
www.ebi.ac.uk/about/news/t...
#bioimaging #microscopy
🧬🔬
If you generate microscopy data or develop AI tools to interpret it, check it these new guidelines:
www.ebi.ac.uk/about/news/t...
#bioimaging #microscopy
🧬🔬
October 13, 2025 at 11:24 AM
AI has so much potential for interpreting biological images, and yet, annotated biological datasets needed to train AI tools remain scarce.
If you generate microscopy data or develop AI tools to interpret it, check it these new guidelines:
www.ebi.ac.uk/about/news/t...
#bioimaging #microscopy
🧬🔬
If you generate microscopy data or develop AI tools to interpret it, check it these new guidelines:
www.ebi.ac.uk/about/news/t...
#bioimaging #microscopy
🧬🔬
Reposted by Judith Garcia-Gonzalez
Thrilled to share that our article in @jofmicroscopy.bsky.social is now accessible online and as open access! If you wonder how to start the analysis of your images, we propose a decision tree to help identify suitable methods. Just follow the link(s)...
#imageanalysis #bioimaging
#imageanalysis #bioimaging
"From cells to pixels: A decision tree for designing bioimage analysis pipelines" by Elnaz Fazeli, Robert Haase, Michael Doube, Kota Miura & David Legland is free-to-view here: doi.org/10.1111/jmi....
September 29, 2025 at 4:17 PM
Thrilled to share that our article in @jofmicroscopy.bsky.social is now accessible online and as open access! If you wonder how to start the analysis of your images, we propose a decision tree to help identify suitable methods. Just follow the link(s)...
#imageanalysis #bioimaging
#imageanalysis #bioimaging
Reposted by Judith Garcia-Gonzalez
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
August 21, 2025 at 2:22 PM
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
Reposted by Judith Garcia-Gonzalez
Over the past few weeks, we've been actively highlighting our projects focused on FAIR image data management and OME-Zarr. Here is a collection, we've collected the related links to the webinars on our news page for you to (re)watch anytime! 🎥🔬: bit.ly/4nHu1DL
#FAIRdata#OMEZarr#Bioimaging
#FAIRdata#OMEZarr#Bioimaging
Recent Webinars Showcasing Our FAIR Image Data Projects - German BioImaging
Website of German BioImaging - Gesellschaft für Mikroskopie und Bildanalyse. Contains also the webpages of I3D:bio, information infrastructure for BioImage Data
bit.ly
July 15, 2025 at 11:13 AM
Over the past few weeks, we've been actively highlighting our projects focused on FAIR image data management and OME-Zarr. Here is a collection, we've collected the related links to the webinars on our news page for you to (re)watch anytime! 🎥🔬: bit.ly/4nHu1DL
#FAIRdata#OMEZarr#Bioimaging
#FAIRdata#OMEZarr#Bioimaging
Reposted by Judith Garcia-Gonzalez
The #ImageData Community Days provided a space for tool exchange, such as CAREamics, HealthRI, TissUUmaps, Microscopy Image Browser, Bia-bob, Pyfix3d & TrackMatev8. 🔬✨
🎥Discover them in our session recordings: www.youtube.com/playlist?lis...
🎥Discover them in our session recordings: www.youtube.com/playlist?lis...
Image Data Community Days
The 'Euro-BioImaging Image Data Community Days' took place in April 2025 and brought together Euro-BioImaging Node staff, researchers, and other experts from...
www.youtube.com
July 16, 2025 at 10:34 AM
The #ImageData Community Days provided a space for tool exchange, such as CAREamics, HealthRI, TissUUmaps, Microscopy Image Browser, Bia-bob, Pyfix3d & TrackMatev8. 🔬✨
🎥Discover them in our session recordings: www.youtube.com/playlist?lis...
🎥Discover them in our session recordings: www.youtube.com/playlist?lis...
Reposted by Judith Garcia-Gonzalez
It's here! ✨
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
July 3, 2025 at 8:44 AM
It's here! ✨
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
Reposted by Judith Garcia-Gonzalez
Spotiflow allows training detection models that generalize across imaging conditions w/o manual parameter tuning. Since the preprint we added lots of things, fast inference for large volumes + many use cases. Check it out at github.com/weigertlab/spotiflow . We hope it will be useful for people!
GitHub - weigertlab/spotiflow: Accurate and efficient spot detection for microscopy data
Accurate and efficient spot detection for microscopy data - weigertlab/spotiflow
github.com
June 6, 2025 at 7:06 PM
Spotiflow allows training detection models that generalize across imaging conditions w/o manual parameter tuning. Since the preprint we added lots of things, fast inference for large volumes + many use cases. Check it out at github.com/weigertlab/spotiflow . We hope it will be useful for people!
Reposted by Judith Garcia-Gonzalez
What do we see when looking at cells under the microscope? 👉Some are bigger than others, some are elongated and align with the neighbors & others seem to move. Cool, right? But wouldn't it be cooler to quantify these observations?
I'm @juliaeckert.bsky.social. Let's explore some analysis software!
I'm @juliaeckert.bsky.social. Let's explore some analysis software!
June 8, 2025 at 7:01 AM
What do we see when looking at cells under the microscope? 👉Some are bigger than others, some are elongated and align with the neighbors & others seem to move. Cool, right? But wouldn't it be cooler to quantify these observations?
I'm @juliaeckert.bsky.social. Let's explore some analysis software!
I'm @juliaeckert.bsky.social. Let's explore some analysis software!
Reposted by Judith Garcia-Gonzalez
NFDI4BIOIMAGE experts will share best practices for #FAIR #bioimaging data in the @ebi.embl.org webinar series from May 14 to July 2, 2025. Topics of the series include #DataManagement, open formats, public archives, and more. Registration is free.
👉 www.ebi.ac.uk/training/eve...
👉 www.ebi.ac.uk/training/eve...
May 12, 2025 at 10:32 AM
NFDI4BIOIMAGE experts will share best practices for #FAIR #bioimaging data in the @ebi.embl.org webinar series from May 14 to July 2, 2025. Topics of the series include #DataManagement, open formats, public archives, and more. Registration is free.
👉 www.ebi.ac.uk/training/eve...
👉 www.ebi.ac.uk/training/eve...
Reposted by Judith Garcia-Gonzalez
If you are looking to do GPU deconvolution in Fiji checkout the new updates to CLIJ (OpenCL for ImageJ) deconvolution. @nkiaru.bsky.social has done updates to the tiled deconvolution and integrated with BigDataViewer, and I've added a new script for batch processing. forum.image.sc/t/clij-openc...
CLIJ (OpenCL for ImageJ) Deconvolution Update!
Hi In recent months @NicoKiaru has done a lot of work on tiled deconvolution and also helped get clijx-deconvolution onto a Fiji Update site. So we are happy to announce it is now much easier to rel...
forum.image.sc
March 12, 2025 at 5:00 PM
If you are looking to do GPU deconvolution in Fiji checkout the new updates to CLIJ (OpenCL for ImageJ) deconvolution. @nkiaru.bsky.social has done updates to the tiled deconvolution and integrated with BigDataViewer, and I've added a new script for batch processing. forum.image.sc/t/clij-openc...
Reposted by Judith Garcia-Gonzalez
openRxiv has arrived!
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
March 11, 2025 at 1:18 PM
openRxiv has arrived!
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
Reposted by Judith Garcia-Gonzalez
🌍 The partnership between @ai4life.bsky.social and AI4EOSC is transforming bioimaging with an accessible and scalable AI Marketplace.
Researchers can now deploy models effortlessly, enhancing scientific reproducibility. 🔬🚀
Learn more📲: bit.ly/419BhPJ
Researchers can now deploy models effortlessly, enhancing scientific reproducibility. 🔬🚀
Learn more📲: bit.ly/419BhPJ
February 10, 2025 at 1:02 PM
🌍 The partnership between @ai4life.bsky.social and AI4EOSC is transforming bioimaging with an accessible and scalable AI Marketplace.
Researchers can now deploy models effortlessly, enhancing scientific reproducibility. 🔬🚀
Learn more📲: bit.ly/419BhPJ
Researchers can now deploy models effortlessly, enhancing scientific reproducibility. 🔬🚀
Learn more📲: bit.ly/419BhPJ
Reposted by Judith Garcia-Gonzalez
This story was only possible through true team effort. Team Kalanchoë with Xin at the forefront. @jameshartwell.bsky.social, the most generous scientist who shared resources and answered countless questions. Read about MUTE during stomatal development in Kalanchoë www.biorxiv.org/content/10.1...
December 28, 2024 at 2:38 PM
This story was only possible through true team effort. Team Kalanchoë with Xin at the forefront. @jameshartwell.bsky.social, the most generous scientist who shared resources and answered countless questions. Read about MUTE during stomatal development in Kalanchoë www.biorxiv.org/content/10.1...
Reposted by Judith Garcia-Gonzalez
Happy #MicroscopyMonday!
The recordings of the #Virtual #I2K2024 workshops are available now
tinyurl.com/VirtualI2K20...
Thanks to all who presented!
Please re-share! 2022 and 2023 content available too:
www.youtube.com/@I2KConference
The recordings of the #Virtual #I2K2024 workshops are available now
tinyurl.com/VirtualI2K20...
Thanks to all who presented!
Please re-share! 2022 and 2023 content available too:
www.youtube.com/@I2KConference
November 25, 2024 at 6:44 PM
Happy #MicroscopyMonday!
The recordings of the #Virtual #I2K2024 workshops are available now
tinyurl.com/VirtualI2K20...
Thanks to all who presented!
Please re-share! 2022 and 2023 content available too:
www.youtube.com/@I2KConference
The recordings of the #Virtual #I2K2024 workshops are available now
tinyurl.com/VirtualI2K20...
Thanks to all who presented!
Please re-share! 2022 and 2023 content available too:
www.youtube.com/@I2KConference
Reposted by Judith Garcia-Gonzalez
🆕 We have updated our preprint in @biorxivpreprint.bsky.social
📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it!
"BiaPy: Accessible deep learning on bioimages"
www.biorxiv.org/content/10.1...
📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it!
"BiaPy: Accessible deep learning on bioimages"
www.biorxiv.org/content/10.1...
BiaPy: Accessible deep learning on bioimages
BiaPy is an open-source library and application that streamlines the use of common deep learning approaches for bioimage analysis. Designed to simplify technical complexities, it offers an intuitive i...
www.biorxiv.org
November 16, 2024 at 9:57 AM
🆕 We have updated our preprint in @biorxivpreprint.bsky.social
📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it!
"BiaPy: Accessible deep learning on bioimages"
www.biorxiv.org/content/10.1...
📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it!
"BiaPy: Accessible deep learning on bioimages"
www.biorxiv.org/content/10.1...
Reposted by Judith Garcia-Gonzalez
My #BioimageTooloftheDay is the awesome 3Dscript that I use to make video of 3D/4D microscopy data www.nature.com/articles/s41...
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax - Nature Methods
Nature Methods - 3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax
www.nature.com
November 16, 2024 at 8:42 AM
My #BioimageTooloftheDay is the awesome 3Dscript that I use to make video of 3D/4D microscopy data www.nature.com/articles/s41...
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
Reposted by Judith Garcia-Gonzalez
Check this recent talk from collaborator and pal @guijacquemet.bsky.social at UCL: fundamental cell biology tackled with cutting-edge image analysis methods www.youtube.com/watch?v=KTdZ...
Dr Guillaume Jacquemet on studying cancer cell metastasis in the era of deep learning for microscopy
YouTube video by UCL Cell and Developmental Biology
www.youtube.com
November 15, 2024 at 10:10 AM
Check this recent talk from collaborator and pal @guijacquemet.bsky.social at UCL: fundamental cell biology tackled with cutting-edge image analysis methods www.youtube.com/watch?v=KTdZ...
Reposted by Judith Garcia-Gonzalez
I will try to take on the challenge to highlight some of the cool bioimage analysis tools we use all the time. #BioimageTooloftheDay
I will start with ijp-LaRoMe, a very nifty Fiji plugin that I use all the time to convert ROI to label images and vice versa
github.com/BIOP/ijp-LaR...
I will start with ijp-LaRoMe, a very nifty Fiji plugin that I use all the time to convert ROI to label images and vice versa
github.com/BIOP/ijp-LaR...
GitHub - BIOP/ijp-LaRoMe: some useful function to get Label from ROIs and vice versa , and more!
some useful function to get Label from ROIs and vice versa , and more! - BIOP/ijp-LaRoMe
github.com
November 11, 2024 at 7:13 AM
I will try to take on the challenge to highlight some of the cool bioimage analysis tools we use all the time. #BioimageTooloftheDay
I will start with ijp-LaRoMe, a very nifty Fiji plugin that I use all the time to convert ROI to label images and vice versa
github.com/BIOP/ijp-LaR...
I will start with ijp-LaRoMe, a very nifty Fiji plugin that I use all the time to convert ROI to label images and vice versa
github.com/BIOP/ijp-LaR...
Reposted by Judith Garcia-Gonzalez
Need a 5-15 minute break from doomscrolling? (You know you do!) Take 5 minutes and tell us how to make #bioimageanalysis #imageanalysis better!
Have you ever analyzed a #microscope image before- even just a single one? Please take our survey on progress and places to still improve for image analysis software! #microscopy #imageanalysis #bioimageanalysis forum.image.sc/t/2024-image...
2024 Image Analysis Survey
The Center for Open Bioimage Analysis , Bioimaging North America , the Royal Microscopical Society, and the Global Bioimage Analysts’ Society have now released a new and improved edition of our biannu...
forum.image.sc
November 6, 2024 at 12:05 AM
Need a 5-15 minute break from doomscrolling? (You know you do!) Take 5 minutes and tell us how to make #bioimageanalysis #imageanalysis better!
Reposted by Judith Garcia-Gonzalez
If you didn't yet have enough good reasons to share your bioimage data, Matthew, Josh (@joshmoore.bsky.social), Erin, Assaf and I are here with squirrel drawings to convince you that you should do it: journals.biologists.com/jcs/article/...
Making the most of bioimaging data through interdisciplinary interactions
Summary: A proposal for actions needed to consolidate the development of an inclusive and open culture of data sharing in bioimaging and a highlight of the promising outlook of multidisciplinary scien...
journals.biologists.com
October 25, 2024 at 12:21 PM
If you didn't yet have enough good reasons to share your bioimage data, Matthew, Josh (@joshmoore.bsky.social), Erin, Assaf and I are here with squirrel drawings to convince you that you should do it: journals.biologists.com/jcs/article/...