Anwai Archit
@anwaiarchit.bsky.social
PhD Candidate at @cppape.bsky.social lab.
Pinned
Anwai Archit
@anwaiarchit.bsky.social
· Feb 12
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
μsam is live in Nature Methods!🥳
Huge thanks to @cppape.bsky.social for being the absolute best PI, guiding me through every step in this journey, @ritastrack.bsky.social for amazing handling of our paper & all reviewers for helping us strengthen μsam.
Go check our tool and paper right away!😉🧵
Huge thanks to @cppape.bsky.social for being the absolute best PI, guiding me through every step in this journey, @ritastrack.bsky.social for amazing handling of our paper & all reviewers for helping us strengthen μsam.
Go check our tool and paper right away!😉🧵
Reposted by Anwai Archit
Preprint alert! CochleaNet, our framework for analyzing light-sheet data of the cochlea. It consists of three networks to segment spiral ganglion neurons, inner hair cells, and to detect synapses. See rendering of a full cochlea in the image, find the preprint at doi.org/10.1101/2025....
November 18, 2025 at 7:59 AM
Preprint alert! CochleaNet, our framework for analyzing light-sheet data of the cochlea. It consists of three networks to segment spiral ganglion neurons, inner hair cells, and to detect synapses. See rendering of a full cochlea in the image, find the preprint at doi.org/10.1101/2025....
Reposted by Anwai Archit
Don’t miss Elena’s (from @ilastik-team.bsky.social lab) brilliant work @ #ICCV2025 with @anwaiarchit.bsky.social & @cppape.bsky.social poster 292 @ 11:15AM 🔬They tackle segmentation of massive 3D microscopy images & show how BatchRenorm removes tiling artifacts boosting transferability and clarity🌺
October 22, 2025 at 8:23 PM
Don’t miss Elena’s (from @ilastik-team.bsky.social lab) brilliant work @ #ICCV2025 with @anwaiarchit.bsky.social & @cppape.bsky.social poster 292 @ 11:15AM 🔬They tackle segmentation of massive 3D microscopy images & show how BatchRenorm removes tiling artifacts boosting transferability and clarity🌺
Reposted by Anwai Archit
Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published:
www.molbiolcell.org/doi/full/10....
www.molbiolcell.org/doi/full/10....
October 17, 2025 at 11:09 AM
Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published:
www.molbiolcell.org/doi/full/10....
www.molbiolcell.org/doi/full/10....
Reposted by Anwai Archit
Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues.
The paper: arxiv.org/abs/2503.19545 1/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
October 9, 2025 at 12:56 PM
Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues.
The paper: arxiv.org/abs/2503.19545 1/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
Reposted by Anwai Archit
Data is the key to AI advances in biology and "Still, when it comes to data, nothing compares to the real thing." An important editorial in Nature methods with a nice little shout out to microSAM:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Calling all data - Nature Methods
As life sciences research becomes enmeshed in the age of AI, real experimental data are more valuable than ever.
www.nature.com
August 7, 2025 at 4:06 PM
Data is the key to AI advances in biology and "Still, when it comes to data, nothing compares to the real thing." An important editorial in Nature methods with a nice little shout out to microSAM:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Anwai Archit
Anwai represented the lab at MIDL very well! Read his thread for details on our two latest papers on foundation models for microscopy, histopathology and medical imaging.
We presented our latest work on "PathoSAM" and "Late PEFT" last week at #MIDL2025 (Salt Lake City)!
The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵
The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵
July 16, 2025 at 7:54 PM
Anwai represented the lab at MIDL very well! Read his thread for details on our two latest papers on foundation models for microscopy, histopathology and medical imaging.
We presented our latest work on "PathoSAM" and "Late PEFT" last week at #MIDL2025 (Salt Lake City)!
The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵
The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵
July 16, 2025 at 5:46 PM
We presented our latest work on "PathoSAM" and "Late PEFT" last week at #MIDL2025 (Salt Lake City)!
The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵
The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵
Reposted by Anwai Archit
Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.
July 7, 2025 at 11:46 AM
Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.
Reposted by Anwai Archit
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
June 16, 2025 at 3:53 PM
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
Reposted by Anwai Archit
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression
Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...
rdcu.be
June 6, 2025 at 6:58 PM
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Reposted by Anwai Archit
A nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression - Nature Methods
Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in both iST and live imag...
www.nature.com
June 6, 2025 at 5:29 PM
A nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...
Reposted by Anwai Archit
Announcing the new release v1.4.0 of microSAM. The main changes are:
1. Simplified installation on windows.
2. Preliminary support for automatic tracking.
3. Improved interface for model selection.
Read on for a quick summary of the changes.
1. Simplified installation on windows.
2. Preliminary support for automatic tracking.
3. Improved interface for model selection.
Read on for a quick summary of the changes.
March 28, 2025 at 7:08 PM
Announcing the new release v1.4.0 of microSAM. The main changes are:
1. Simplified installation on windows.
2. Preliminary support for automatic tracking.
3. Improved interface for model selection.
Read on for a quick summary of the changes.
1. Simplified installation on windows.
2. Preliminary support for automatic tracking.
3. Improved interface for model selection.
Read on for a quick summary of the changes.
Reposted by Anwai Archit
@anwaiarchit.bsky.social & @cppape.bsky.social demonstrating the power of micro-sam, the napari plugin for the microscopy segment anything model, in their awesome workshop at the #TiM2025 conference in Münsingen. 🔬🦠💻
March 19, 2025 at 9:08 AM
@anwaiarchit.bsky.social & @cppape.bsky.social demonstrating the power of micro-sam, the napari plugin for the microscopy segment anything model, in their awesome workshop at the #TiM2025 conference in Münsingen. 🔬🦠💻
Reposted by Anwai Archit
Our March issue is now live! 🥳
nature.com/nmeth/volume...
The cover represents the process of cell and organelle segmentation by Segment Anything for Microscopy.
Paper here: nature.com/articles/s41...
Cover by Sebastian von Haaren.
nature.com/nmeth/volume...
The cover represents the process of cell and organelle segmentation by Segment Anything for Microscopy.
Paper here: nature.com/articles/s41...
Cover by Sebastian von Haaren.
March 13, 2025 at 3:53 PM
Our March issue is now live! 🥳
nature.com/nmeth/volume...
The cover represents the process of cell and organelle segmentation by Segment Anything for Microscopy.
Paper here: nature.com/articles/s41...
Cover by Sebastian von Haaren.
nature.com/nmeth/volume...
The cover represents the process of cell and organelle segmentation by Segment Anything for Microscopy.
Paper here: nature.com/articles/s41...
Cover by Sebastian von Haaren.
Another feather for Segment Anything for Microscopy. We made it to the cover for @naturemethods.bsky.social!
And all thanks to our amazing @haarensv.bsky.social for this! <3
And all thanks to our amazing @haarensv.bsky.social for this! <3
A small but special moment: My illustration is on the cover of the March issue of Nature Methods!
A huge hug to @anwaiarchit.bsky.social and @cppape.bsky.social — it was a pleasure to work alongside you on this!
www.nature.com/nmeth/volume...
A huge hug to @anwaiarchit.bsky.social and @cppape.bsky.social — it was a pleasure to work alongside you on this!
www.nature.com/nmeth/volume...
March 13, 2025 at 4:25 PM
Another feather for Segment Anything for Microscopy. We made it to the cover for @naturemethods.bsky.social!
And all thanks to our amazing @haarensv.bsky.social for this! <3
And all thanks to our amazing @haarensv.bsky.social for this! <3
Reposted by Anwai Archit
Automatische Zellanalyse mit #KI: Forschende trainierten eine bestehende, KI-basierte Software neu. Das Modell „Segment Anything for Microscopy“ kann Bilder von Geweben, Zellen und anderen Strukturen genau segmentieren: s.gwdg.de/HqkMz2; s.gwdg.de/iTejKW
Forschungsteam mit bsky.app/profile/cppa...
Forschungsteam mit bsky.app/profile/cppa...
February 26, 2025 at 10:42 AM
Automatische Zellanalyse mit #KI: Forschende trainierten eine bestehende, KI-basierte Software neu. Das Modell „Segment Anything for Microscopy“ kann Bilder von Geweben, Zellen und anderen Strukturen genau segmentieren: s.gwdg.de/HqkMz2; s.gwdg.de/iTejKW
Forschungsteam mit bsky.app/profile/cppa...
Forschungsteam mit bsky.app/profile/cppa...
That's a wrap for #EMBLDeepLearning 🌠
A huge thank you to everyone who attended this advanced course 🙌 We hope the hands-on element of applying deep learning-based methods to your own data and image analysis problems was useful. Until next time!
A huge thank you to everyone who attended this advanced course 🙌 We hope the hands-on element of applying deep learning-based methods to your own data and image analysis problems was useful. Until next time!
February 24, 2025 at 9:49 PM
Thank you @unigoettingen.bsky.social for the feature!😍
μsam got some super cool feature updates last week. Don't wait for the next release, go check us out now!
github.com/computationa...
μsam got some super cool feature updates last week. Don't wait for the next release, go check us out now!
github.com/computationa...
Automatic cell analysis using #AI
Researchers retrained existing AI-based software on over 17,000 microscopy images with over 2 million structures to develop this new model - Segment Anything for Microscopy: www.uni-goettingen.de/en/3240.html...
#NatureMethods research: doi.org/10.1038/s415...
Researchers retrained existing AI-based software on over 17,000 microscopy images with over 2 million structures to develop this new model - Segment Anything for Microscopy: www.uni-goettingen.de/en/3240.html...
#NatureMethods research: doi.org/10.1038/s415...
February 24, 2025 at 11:56 AM
Thank you @unigoettingen.bsky.social for the feature!😍
μsam got some super cool feature updates last week. Don't wait for the next release, go check us out now!
github.com/computationa...
μsam got some super cool feature updates last week. Don't wait for the next release, go check us out now!
github.com/computationa...
Reposted by Anwai Archit
Because we have seen these improvements and due to popular demand, cc @ritastrack.bsky.social @jianxuchen.bsky.social, we have decided to start a call for community data submission to further improve our models: computational-cell-analytics.github.io/micro-sam/mi... . Looking forward to any feedback
micro_sam API documentation
computational-cell-analytics.github.io
February 21, 2025 at 10:36 AM
Because we have seen these improvements and due to popular demand, cc @ritastrack.bsky.social @jianxuchen.bsky.social, we have decided to start a call for community data submission to further improve our models: computational-cell-analytics.github.io/micro-sam/mi... . Looking forward to any feedback
Reposted by Anwai Archit
Our next micro_sam release is here! We have a new model for light microscopy, that massively improves for automatic segmentation! See the qualitative and quantitative comparison in the images, v2 is our previous version, v3 is the new one.
February 21, 2025 at 10:36 AM
Our next micro_sam release is here! We have a new model for light microscopy, that massively improves for automatic segmentation! See the qualitative and quantitative comparison in the images, v2 is our previous version, v3 is the new one.
Reposted by Anwai Archit
Help improve MicroSAM!
Because we have seen these improvements and due to popular demand, cc @ritastrack.bsky.social @jianxuchen.bsky.social, we have decided to start a call for community data submission to further improve our models: computational-cell-analytics.github.io/micro-sam/mi... . Looking forward to any feedback
micro_sam API documentation
computational-cell-analytics.github.io
February 21, 2025 at 2:08 PM
Help improve MicroSAM!
Reposted by Anwai Archit
I actually tested these two and also SamCell (recently on Biorxiv). Here's the quick and dirty results - might still be finetuned, and I might have not always picked the best settings.
So much happening in the segmentation space for bioimage analysis. These two papers that were published online today really stood out to me as noteworthy (a thread).
February 16, 2025 at 9:29 PM
I actually tested these two and also SamCell (recently on Biorxiv). Here's the quick and dirty results - might still be finetuned, and I might have not always picked the best settings.
Reposted by Anwai Archit
Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more.
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
February 21, 2025 at 6:57 AM
Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more.
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
Reposted by Anwai Archit
🎤 Another speaker joins #TiM2025!
We’re thrilled to announce @ritastrack.bsky.social as a new speaker, delivering an exciting talk on Wednesday. Huge thanks to her for joining us! Stay tuned for more updates on our TiM page: bit.ly/3BPN9fB
We’re thrilled to announce @ritastrack.bsky.social as a new speaker, delivering an exciting talk on Wednesday. Huge thanks to her for joining us! Stay tuned for more updates on our TiM page: bit.ly/3BPN9fB
February 13, 2025 at 10:34 AM
🎤 Another speaker joins #TiM2025!
We’re thrilled to announce @ritastrack.bsky.social as a new speaker, delivering an exciting talk on Wednesday. Huge thanks to her for joining us! Stay tuned for more updates on our TiM page: bit.ly/3BPN9fB
We’re thrilled to announce @ritastrack.bsky.social as a new speaker, delivering an exciting talk on Wednesday. Huge thanks to her for joining us! Stay tuned for more updates on our TiM page: bit.ly/3BPN9fB