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Anwai Archit

@anwaiarchit.bsky.social

82 followers 150 following 25 posts

PhD Candidate at @cppape.bsky.social lab.

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Anwai Archit @anwaiarchit.bsky.social · Feb 12

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!😉🧵

Constantin Pape @cppape.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...

Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.

Reposted by Anwai Archit

Constantin Pape @cppape.bsky.social · Aug 7

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...

Calling all data - Nature Methods

As life sciences research becomes enmeshed in the age of AI, real experimental data are more valuable than ever.

Reposted by Anwai Archit

Constantin Pape @cppape.bsky.social · Jul 16

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.

Anwai Archit @anwaiarchit.bsky.social · Jul 16

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!🧵

Anwai Archit @anwaiarchit.bsky.social · Jul 16

There are exciting opportunities and foreseeable clinical applications of vision foundation models for biomedical image analysis! The MIDL Community did seem excited, and so are we! (some amazing follow-up applications coming soon, keep an eye open 😉)

Anwai Archit @anwaiarchit.bsky.social · Jul 16

And both of our efforts and these beautiful presentations at #MIDL2025 have been successful due to immense efforts from our amazing lab members @caroteu.bsky.social and Titus Griebel. And of-course @cppape.bsky.social being the absolute best PI, as always (I can't say this enough tbh)!

Anwai Archit @anwaiarchit.bsky.social · Jul 16

And sticking to our @cppape.bsky.social lab's theme of rocking in the open-source world, all the models and code are completely open to use and easy to access. You can take @midl-conference.bsky.social's word on this! 😉

PathoSAM: github.com/computationa...

Late PEFT: github.com/computationa...

Anwai Archit @anwaiarchit.bsky.social · Jul 16

Next, we introduce a novel finetuning paradigm for foundation models "Late PEFT", inspired by our striking observations of PEFT's memory requirements, questioning: "Are PEFT methods Resource Efficient?"

We have an answer: PEFT "can be resource efficient"! Check out more at: doi.org/10.48550/arX...

Parameter Efficient Fine-Tuning of Segment Anything Model for Biomedical Imaging

Segmentation is an important analysis task for biomedical images, enabling the study of individual organelles, cells or organs. Deep learning has massively improved segmentation methods, but challenge...

Anwai Archit @anwaiarchit.bsky.social · Jul 16

To begin with, here's "PathoSAM", our foundation model for nucleus segmentation in histopathology, presented as an Oral! (and my very first one).

If you want a SOTA model for interactive and automatic segmentation for your histopathology images, go check out the paper now doi.org/10.48550/arX...

Anwai Archit @anwaiarchit.bsky.social · Jul 16

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!🧵

Reposted by Anwai Archit

Constantin Pape @cppape.bsky.social · Jul 7

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

Constantin Pape @cppape.bsky.social · Jun 16

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.

Reposted by Anwai Archit

Albert Dominguez Mantes @albertdm.bsky.social · Jun 6

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)

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...

Anwai Archit @anwaiarchit.bsky.social · Jun 8

Congratulations @maweigert.bsky.social and @albertdm.bsky.social 🥳

Reposted by Anwai Archit

Nature Methods @natmethods.nature.com · Jun 6

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...

Reposted by Anwai Archit

Constantin Pape @cppape.bsky.social · Mar 28

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.

Reposted by Anwai Archit

Chris Schmidt @schmchris.bsky.social · Mar 19

@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

Nature Methods @natmethods.nature.com · Mar 13

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.

Anwai Archit @anwaiarchit.bsky.social · Mar 13

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

Sebastian von Haaren @haarensv.bsky.social · Mar 13

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...

Anwai Archit @anwaiarchit.bsky.social · Mar 3

Hi @psobolewskiphd.bsky.social,
It's under the same name in our GUI model list. With the latest version installed, this will be stored in cache automatically!

Reposted by Anwai Archit

Uni Göttingen @uni-goettingen.de · Feb 26

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...

Pflanzenzellen, die mit einem Fluoreszenzmikroskop aufgenommen und mit dem Modell automatisch segmentiert wurden. Die zugrunde liegenden Daten sind dreidimensional und das Bild zeigt eine Darstellung der segmentierten Zellen, die jeweils durch eine andere Farbe repräsentiert werden.

Foto: Nature Methods: 10.1038/s41592-024-02580-4

Segmentierung von Zellen in der Lichtmikroskopie mit μSAM. Das Bild zeigt, wie Zellen in der Phasenkontrastmikroskopie mit μSAM segmentiert werden können. Grüne Punkte und Kästchen zeigen die Benutzereingabe und farbige Masken die entsprechende Vorhersage des Modells.

Foto: Erstellt von Anwai Archit mit dem μSAM-Tool, verfügbar in Nature Methods: 10.1038/s41592-024-02580-4

Anwai Archit @anwaiarchit.bsky.social · Feb 24

It was soooo much fun to brainstorm solutions with everyone, together!❤️

#EMBLDeepLearning

EMBL Events @events.embl.org · Feb 21

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!

Anwai Archit @anwaiarchit.bsky.social · Feb 24

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...

Uni Göttingen @uni-goettingen.de · Feb 24

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...

This is a flat grey image with cell structures in darker grey. Some of the cells are coloured and shown in green boxes. This image - Segmentation of electron microscopy images with μSAM - shows how the model can segment nuclei, with points and boxes from the user and the corresponding masks predicted by the model.
Photo: The underlying image comes from data published in Cell (S0092-8674(21)00876-X). Image created by Anwai Archit using the μSAM tool.

This is a three dimensional representation with a cross-section showing dark patches in different colours and the outside of the structure with bright different colours (green, purple, blue, dark pink, yellow, orange). The image shows plant cells acquired with a fluorescence microscope that were segmented automatically with the model. The underlying data is three-dimensional and the image shows a rendering of the segmented cells, each represented by a different colour.
Image from: Nature Methods: s41592-021-01249-6

Reposted by Anwai Archit

Constantin Pape @cppape.bsky.social · Feb 21

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

Reposted by Anwai Archit

Constantin Pape @cppape.bsky.social · Feb 21

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

Rita Strack @ritastrack.bsky.social · Feb 21

Help improve MicroSAM!

Constantin Pape @cppape.bsky.social · Feb 21

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

Reposted by Anwai Archit

Josh Moore @joshmoore.bsky.social · Feb 21

Look at all of those #OMEZarrs! 🤩

Screenshare of a 3D rendering in neuroglancer.

Available under "View tomogram" on the following page: https://cryoetdataportal.czscience.com/runs/16497?deposition-id=10330