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69 changes: 39 additions & 30 deletions _bibliography/papers.bib
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Expand Up @@ -3,6 +3,14 @@

@string{aps = {American Physical Society,}}

@inproceedings{archit2024vimunet,
title={ViM-{UN}et: Vision Mamba for Biomedical Segmentation},
author={Anwai Archit and Constantin Pape},
booktitle={Medical Imaging with Deep Learning},
year={2024},
url={https://openreview.net/forum?id=PYNwysgFeP}
}

@article{archit2025segment,
title={Segment anything for microscopy},
author={Archit, Anwai and Freckmann, Luca and Nair, Sushmita and Khalid, Nabeel and Hilt, Paul and Rajashekar, Vikas and Freitag, Marei and Teuber, Carolin and Spitzner, Melanie and Tapia Contreras, Constanza and Buckley, Genevieve and von Haaren, Sebastian, and Gupta, Sagnik and Grade, Marian and Wirth, Matthias and Schneider, Günter and Dengel, Andreas and Ahmed, Sheraz and Pape, Constantin},
Expand All @@ -17,6 +25,18 @@ @article{archit2025segment
selected={true},
}

@article{JeremiasPape+2025+203+213,
url = {https://doi.org/10.1515/mim-2024-0021},
title = {Stamped counting for biomedical images},
author = {Julia Jeremias and Constantin Pape},
pages = {203--213},
volume = {2},
number = {2},
journal = {Methods in Microscopy},
doi = {doi:10.1515/mim-2024-0021},
year = {2025},
}

@article{muth2025synapsenet,
title={SynapseNet: deep learning for automatic synapse reconstruction},
author={Muth, Sarah and Moschref, Frederieke and Freckmann, Luca and Mutschall, Sophia and Hojas-Garcia-Plaza, Ines and Bahr, Julius N and Petrovic, Arsen and Do, Thanh Thao and Schwarze, Valentin and Archit, Anwai and Weyand, Kirsten and Michanski, Susann and Maus, Lydia and Imig†, Cordelia and Hintze, Anika and Brose, Nils and Wichmann, Carolin and Fernandez-Busnadiego, Ruben and Moser, Tobias and Rizzoli, Silvio O. and Cooper, Benjamin H. and Pape, Constantin},
Expand All @@ -30,46 +50,35 @@ @article{muth2025synapsenet
selected={true}
}

@misc{griebel2025segmenthistopathology,
title={Segment Anything for Histopathology},
@inproceedings{griebel2025segment,
title={Segment Anything for Histopathology},
author={Titus Griebel and Anwai Archit and Constantin Pape},
booktitle={Medical Imaging with Deep Learning},
year={2025},
eprint={2502.00408},
archivePrefix={arXiv},
primaryClass={eess.IV},
url={https://arxiv.org/abs/2502.00408},
url={https://openreview.net/forum?id=EWGV97ESaP}
}

@misc{teuber2025parameterefficientfinetuningsegment,
title={Parameter Efficient Fine-Tuning of Segment Anything Model for Biomedical Imaging},
@inproceedings{teuber2025parameter,
title={Parameter Efficient Fine-Tuning of Segment Anything Model for Biomedical Imaging},
author={Carolin Teuber and Anwai Archit and Constantin Pape},
booktitle={Medical Imaging with Deep Learning},
year={2025},
eprint={2502.00418},
archivePrefix={arXiv},
primaryClass={cs.CV},
url={https://arxiv.org/abs/2502.00418},
url={https://openreview.net/forum?id=TWPnpixpW2}
}

@article{JeremiasPape+2025+203+213,
url = {https://doi.org/10.1515/mim-2024-0021},
title = {Stamped counting for biomedical images},
author = {Julia Jeremias and Constantin Pape},
pages = {203--213},
volume = {2},
number = {2},
journal = {Methods in Microscopy},
doi = {doi:10.1515/mim-2024-0021},
year = {2025},
lastchecked = {2025-10-10}
}

@misc{archit2025probabilisticdomainadaptationbiomedical,
@article{archit2025probabilisticdomainadaptationbiomedical,
title={Probabilistic Domain Adaptation for Biomedical Image Segmentation},
author={Anwai Archit and Constantin Pape},
year={2025},
eprint={2303.11790},
archivePrefix={arXiv},
primaryClass={cs.CV},
url={https://arxiv.org/abs/2303.11790},
publisher={ICCV Workshops (BioImage Computing)},
url={https://arxiv.org/abs/2303.11790},
}

@misc{archit2025medicosam,
doi = {10.48550/ARXIV.2501.11734},
url = {https://arxiv.org/abs/2501.11734},
author = {Archit, Anwai and Freckmann, Luca and Pape, Constantin},
title = {MedicoSAM: Towards foundation models for medical image segmentation},
publisher = {arXiv},
year = {2025},
}
4 changes: 2 additions & 2 deletions _pages/about.md
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layout: about
title: about
permalink: /
subtitle: <a href='#'>Institute of Computer Science</a> Georg-August University Göttingen
subtitle: <a href="https://www.uni-goettingen.de/en/institute+of+computer+science/619480.html">Institute of Computer Science</a>, Georg-August Universität Göttingen

profile:
align: right
Expand All @@ -29,7 +29,7 @@ latest_posts:

We develop deep learning and AI methods for biology and medicine. We mainly develop computer vision methods for the analysis of biomedical image data, but are also interested in combining different modalities, such as image and omics data. Our two main research areas are building (vision) foundation models for biology and medicine and protein structure analysis in cryogenic electron microscopy and in super-resolution microscopy. We apply these methods to challenging biomedical research questions in collaboration with life scientists.

We are dedicated to open source and open science and we are involved in multiple related efforts. In particular, the [bioimage.io modelzoo](https://bioimage.io/#/models), a resource to share deep learning models for microscopy image analysis and [ome.ngff](https://www.nature.com/articles/s41592-021-01326-w), a new image data format that supports efficient storage of large data and on-demand access in the cloud, and [MoBIE](https://mobie.github.io), a Fiji plugin for exploring and sharing large multi-modal image data.
We are dedicated to open source and open science and we are involved in multiple related efforts. In particular, the [BioImage.IO ModelZoo](https://bioimage.io/#/models), a resource to share deep learning models for microscopy image analysis and [OME.NGFF](https://www.nature.com/articles/s41592-021-01326-w), a new image data format that supports efficient storage of large data and on-demand access in the cloud, and [MoBIE](https://mobie.github.io), a Fiji plugin for exploring and sharing large multi-modal image data.

Our research is funded and supported by the DFG through a Sachbeihilfe, the [SFB1286 on Quantitative Synaptology](https://www.sfb1286.de), and the Multiscale Bioimaging Cluster of Excellence ([MBExC](https://mbexc.de/de/)). We are part of the [CAIMed](https://caimed.de/en/) consortium.

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4 changes: 3 additions & 1 deletion _pages/about/anwai.md
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@@ -1,2 +1,4 @@
**Anwai Archit** \
PhD student
PhD Student

Developing Vision Foundation Models for Bio(medical)-Image Analysis
8 changes: 4 additions & 4 deletions _pages/profiles.md
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<p>Room 2.???</p>
<p><a href="mailto:[email protected]">[email protected]</a></p>
- align: right
image: generic_profile.jpg
image: anwai.jpeg
content: /about/anwai.md
image_circular: true # crops the image to make it circular
more_info: >
<p>Room 1.125?</p>
<p>mail@uni-goettingen.de</p>
<p>Room 1.123</p>
<p><a href="mailto:anwai.archit@uni-goettingen.de">[email protected]</a></p>
- align: left
image: generic_profile.jpg
content: /about/sushmita.md
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content: /about/martin.md
image_circular: true # crops the image to make it circular
more_info: >
<p>Room 1.125?</p>
<p>Room 1.123</p>
<p>[email protected]</p>
- align: right
image: generic_profile.jpg
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Binary file added assets/img/anwai.jpeg
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