My #BioimageTooloftheDay is DRMIME
github.com/abnan/DRMIME
It is a very useful tool for aligning images.
I had a lot of fun using it to align zebrafish embryos.
Also available on #ZeroCostDL4Mic
github.com/HenriquesLab...
github.com/abnan/DRMIME
It is a very useful tool for aligning images.
I had a lot of fun using it to align zebrafish embryos.
Also available on #ZeroCostDL4Mic
github.com/HenriquesLab...
November 21, 2024 at 2:42 PM
My #BioimageTooloftheDay is DRMIME
github.com/abnan/DRMIME
It is a very useful tool for aligning images.
I had a lot of fun using it to align zebrafish embryos.
Also available on #ZeroCostDL4Mic
github.com/HenriquesLab...
github.com/abnan/DRMIME
It is a very useful tool for aligning images.
I had a lot of fun using it to align zebrafish embryos.
Also available on #ZeroCostDL4Mic
github.com/HenriquesLab...
My #BioimageTooloftheDay is QuimP a software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
Also makes beautiful cover images warwick.ac.uk/fac/sci/dcs/...
Also makes beautiful cover images warwick.ac.uk/fac/sci/dcs/...
November 22, 2024 at 6:52 PM
My #BioimageTooloftheDay is QuimP a software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
Also makes beautiful cover images warwick.ac.uk/fac/sci/dcs/...
Also makes beautiful cover images warwick.ac.uk/fac/sci/dcs/...
My #BioimageTooloftheDay
is the fantastic Introduction to Bioimage Analysis book by Pete Bankhead
bioimagebook.github.io/index.html
Because seriously, this is awesome
Also how can you get started without a good book
is the fantastic Introduction to Bioimage Analysis book by Pete Bankhead
bioimagebook.github.io/index.html
Because seriously, this is awesome
Also how can you get started without a good book
Introduction to Bioimage Analysis — Introduction to Bioimage Analysis
bioimagebook.github.io
November 30, 2024 at 6:00 PM
My #BioimageTooloftheDay
is the fantastic Introduction to Bioimage Analysis book by Pete Bankhead
bioimagebook.github.io/index.html
Because seriously, this is awesome
Also how can you get started without a good book
is the fantastic Introduction to Bioimage Analysis book by Pete Bankhead
bioimagebook.github.io/index.html
Because seriously, this is awesome
Also how can you get started without a good book
My #BioimageTooloftheDay is TrackMate by @jytinevez.bsky.social and co
We use TrackMate in the lab all the time :)
I was also lucky enough to work with JY on one the iteration of this fantastic Fiji plugin
imagej.net/plugins/trac...
We use TrackMate in the lab all the time :)
I was also lucky enough to work with JY on one the iteration of this fantastic Fiji plugin
imagej.net/plugins/trac...
TrackMate
TrackMate is your buddy for your everyday tracking.
imagej.net
November 18, 2024 at 10:27 AM
My #BioimageTooloftheDay is TrackMate by @jytinevez.bsky.social and co
We use TrackMate in the lab all the time :)
I was also lucky enough to work with JY on one the iteration of this fantastic Fiji plugin
imagej.net/plugins/trac...
We use TrackMate in the lab all the time :)
I was also lucky enough to work with JY on one the iteration of this fantastic Fiji plugin
imagej.net/plugins/trac...
Today I would like to highlight one of our favorite DL-segmentation network: StarDist by @maweigert.bsky.social and colleagues. In my lab we love and use StarDist all the time
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
GitHub - stardist/stardist: StarDist - Object Detection with Star-convex Shapes
StarDist - Object Detection with Star-convex Shapes - stardist/stardist
github.com
November 14, 2024 at 3:34 PM
Today I would like to highlight one of our favorite DL-segmentation network: StarDist by @maweigert.bsky.social and colleagues. In my lab we love and use StarDist all the time
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
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...
My #BioimageTooloftheDay is the fantastic AFT-Alignment tool
www.frontiersin.org/journals/com...
github.com/OakesLab/AFT...
We used the Python implementation to study actin stress fibers organisation in endothelial monolayers
www.frontiersin.org/journals/com...
github.com/OakesLab/AFT...
We used the Python implementation to study actin stress fibers organisation in endothelial monolayers
November 28, 2024 at 8:41 AM
My #BioimageTooloftheDay is the fantastic AFT-Alignment tool
www.frontiersin.org/journals/com...
github.com/OakesLab/AFT...
We used the Python implementation to study actin stress fibers organisation in endothelial monolayers
www.frontiersin.org/journals/com...
github.com/OakesLab/AFT...
We used the Python implementation to study actin stress fibers organisation in endothelial monolayers
As my first post, I am reposting from Twitter our Phindr3D (slightly rewritten).
#BioimageTooloftheDay. Phindr3D is a comprehensive #ShallowLearning framework for automated quantitative phenotyping of #3D #HighContentScreening images. Still valuable in the age of (un)explainable #deeplearning.😉
#BioimageTooloftheDay. Phindr3D is a comprehensive #ShallowLearning framework for automated quantitative phenotyping of #3D #HighContentScreening images. Still valuable in the age of (un)explainable #deeplearning.😉
November 22, 2024 at 7:50 PM
As my first post, I am reposting from Twitter our Phindr3D (slightly rewritten).
#BioimageTooloftheDay. Phindr3D is a comprehensive #ShallowLearning framework for automated quantitative phenotyping of #3D #HighContentScreening images. Still valuable in the age of (un)explainable #deeplearning.😉
#BioimageTooloftheDay. Phindr3D is a comprehensive #ShallowLearning framework for automated quantitative phenotyping of #3D #HighContentScreening images. Still valuable in the age of (un)explainable #deeplearning.😉
My #BioimageTooloftheDay is the Bleach correction ImageJ plugin f1000research.com/articles/9-1...
Very useful yet rarely praised.
Very useful yet rarely praised.
F1000Research Article: Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences.
Read the latest article version by Kota Miura, at F1000Research.
f1000research.com
November 19, 2024 at 7:45 AM
My #BioimageTooloftheDay is the Bleach correction ImageJ plugin f1000research.com/articles/9-1...
Very useful yet rarely praised.
Very useful yet rarely praised.
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 😁
My #BioimageTooloftheDay is the NeuroCyto Luts Fiji plugin by @christlet.bsky.social
A must have collection of very useful LUT to make beautiful merge images
forum.image.sc/t/neurocyto-...
A must have collection of very useful LUT to make beautiful merge images
forum.image.sc/t/neurocyto-...
"NeuroCyto LUTs" update site
Hi, as a LUTs afficionado I have collected and designed a lot of LUTs and found the built-in menu difficult to organize. So I’ve made a specific LUTs menu (using a folder in the “scripts” folder, fill...
forum.image.sc
November 23, 2024 at 9:48 AM
My #BioimageTooloftheDay is the NeuroCyto Luts Fiji plugin by @christlet.bsky.social
A must have collection of very useful LUT to make beautiful merge images
forum.image.sc/t/neurocyto-...
A must have collection of very useful LUT to make beautiful merge images
forum.image.sc/t/neurocyto-...
Today I want to highlight another very useful Fiji plugin Distance Analysis (DiAna).
We used it in a couple of papers already
imagej.net/plugins/dist...
www.sciencedirect.com/science/arti...
#BioimageTooloftheDay
We used it in a couple of papers already
imagej.net/plugins/dist...
www.sciencedirect.com/science/arti...
#BioimageTooloftheDay
Distance Analysis
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.net
November 12, 2024 at 9:16 AM
Today I want to highlight another very useful Fiji plugin Distance Analysis (DiAna).
We used it in a couple of papers already
imagej.net/plugins/dist...
www.sciencedirect.com/science/arti...
#BioimageTooloftheDay
We used it in a couple of papers already
imagej.net/plugins/dist...
www.sciencedirect.com/science/arti...
#BioimageTooloftheDay
My #BioimageTooloftheDay is an easy one: Cellpose by @computingnature.neuromatch.social.ap.brid.gy and colleagues
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
Cellpose 2.0: how to train your own model - Nature Methods
Cellpose 2.0 improves cell segmentation by offering pretrained models that can be fine-tuned using a human-in-the-loop training pipeline and fewer than 1,000 user-annotated regions of interest.
www.nature.com
November 15, 2024 at 4:40 PM
My #BioimageTooloftheDay is an easy one: Cellpose by @computingnature.neuromatch.social.ap.brid.gy and colleagues
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
Today I would like to highlight Labkit from @florianjug.bsky.social lab, one of my favorite pixel classifier. Fiji plugin, very easy to use, GPU accelerated, works on large datasets and has batch processing. imagej.net/plugins/labk...
www.frontiersin.org/journals/com...
#BioimageTooloftheDay
www.frontiersin.org/journals/com...
#BioimageTooloftheDay
Labkit - Intuitive Pixel Classification in Fiji
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.net
November 13, 2024 at 3:36 PM
Today I would like to highlight Labkit from @florianjug.bsky.social lab, one of my favorite pixel classifier. Fiji plugin, very easy to use, GPU accelerated, works on large datasets and has batch processing. imagej.net/plugins/labk...
www.frontiersin.org/journals/com...
#BioimageTooloftheDay
www.frontiersin.org/journals/com...
#BioimageTooloftheDay
My #BioimageTooloftheDay is Kappa, a neat Fiji plugin we used to measure curvature
github.com/fiji/Kappa
github.com/fiji/Kappa
GitHub - fiji/Kappa: A Fiji plugin for Curvature Analysis
A Fiji plugin for Curvature Analysis. Contribute to fiji/Kappa development by creating an account on GitHub.
github.com
November 27, 2024 at 3:17 PM
My #BioimageTooloftheDay is Kappa, a neat Fiji plugin we used to measure curvature
github.com/fiji/Kappa
github.com/fiji/Kappa
My #BioimageTooloftheDay is NANOJ by @henriqueslab.bsky.social lab. NanoJ is super useful for several application including image registration pmc.ncbi.nlm.nih.gov/articles/PMC...
NanoJ had a massive impact on our work and inspired for instance Fast4DReg
NanoJ had a massive impact on our work and inspired for instance Fast4DReg
NanoJ: a high-performance open-source super-resolution microscopy toolbox
Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a lar...
pmc.ncbi.nlm.nih.gov
November 20, 2024 at 1:52 PM
My #BioimageTooloftheDay is NANOJ by @henriqueslab.bsky.social lab. NanoJ is super useful for several application including image registration pmc.ncbi.nlm.nih.gov/articles/PMC...
NanoJ had a massive impact on our work and inspired for instance Fast4DReg
NanoJ had a massive impact on our work and inspired for instance Fast4DReg
My #BioimageTooloftheDay is FPBioimage, a very useful tool for viewing volumetric data
It has a Fiji plugin that works well. The best feature is that you can easily tune rendering quality so you can view larger datasets even without GPU. imagej.net/plugins/fpbi...
fpb.ceb.cam.ac.uk
It has a Fiji plugin that works well. The best feature is that you can easily tune rendering quality so you can view larger datasets even without GPU. imagej.net/plugins/fpbi...
fpb.ceb.cam.ac.uk
Fpbioimage
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.net
November 17, 2024 at 12:40 PM
My #BioimageTooloftheDay is FPBioimage, a very useful tool for viewing volumetric data
It has a Fiji plugin that works well. The best feature is that you can easily tune rendering quality so you can view larger datasets even without GPU. imagej.net/plugins/fpbi...
fpb.ceb.cam.ac.uk
It has a Fiji plugin that works well. The best feature is that you can easily tune rendering quality so you can view larger datasets even without GPU. imagej.net/plugins/fpbi...
fpb.ceb.cam.ac.uk
My #BioimageTooloftheDay is empanada-napari
A very well-designed and useful Napari plugin to segment mitochondria from EM images
github.com/volume-em/em...
www.cell.com/cell-systems...
A very well-designed and useful Napari plugin to segment mitochondria from EM images
github.com/volume-em/em...
www.cell.com/cell-systems...
GitHub - volume-em/empanada-napari: Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari
Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari - volume-em/empanada-napari
github.com
November 25, 2024 at 11:15 AM
My #BioimageTooloftheDay is empanada-napari
A very well-designed and useful Napari plugin to segment mitochondria from EM images
github.com/volume-em/em...
www.cell.com/cell-systems...
A very well-designed and useful Napari plugin to segment mitochondria from EM images
github.com/volume-em/em...
www.cell.com/cell-systems...
My #BioimageTooloftheDay is webKnossos weblium.webknossos.org
It's an awesome annotation tool to do manual segmentation of 3D FIB-SEM dataset. While we cannot quite afford the pro version, the free version will already take you far.
It's an awesome annotation tool to do manual segmentation of 3D FIB-SEM dataset. While we cannot quite afford the pro version, the free version will already take you far.
WEBKNOSSOS: Visualize, share and annotate your large 3D images online
Visualize, share, and annotate your large 3D images online.
Upload your data and share links with colleagues. Collaboratively create skeleton and volume annotations, all from your browser. Optimized f...
weblium.webknossos.org
December 2, 2024 at 4:05 PM
My #BioimageTooloftheDay is webKnossos weblium.webknossos.org
It's an awesome annotation tool to do manual segmentation of 3D FIB-SEM dataset. While we cannot quite afford the pro version, the free version will already take you far.
It's an awesome annotation tool to do manual segmentation of 3D FIB-SEM dataset. While we cannot quite afford the pro version, the free version will already take you far.