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INSTALL.md

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@@ -167,14 +167,12 @@ If you need to manually re-deploy your website to GitHub pages, go to Actions, c
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1. [Use this template -> Create a new repository](https://github.com/new?template_name=al-folio&template_owner=alshedivat).
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2. Netlify: **Add new site** -> **Import an existing project** -> **GitHub** and give Netlify access to the repository you just created.
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3. Netlify: In the deploy settings
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- Set **Branch to deploy** to `main`
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- **Base directory** is empty
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- Set **Build command** to `sed -i "s/^\(baseurl: \).*$/baseurl:/" _config.yml && bundle exec jekyll build`
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- Set **Publish directory** to `_site`
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4. Netlify: Add the following two **environment variables**
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- | Key | Value |
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| -------------- | -------------------------------------------------------------------------------------- |
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| `JEKYLL_ENV` | `production` |

_bibliography/papers.bib

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@string{aps = {American Physical Society,}}
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@book{einstein1920relativity,
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title={Relativity: the Special and General Theory},
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author={Einstein, Albert},
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year={1920},
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publisher={Methuen & Co Ltd},
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html={relativity.html}
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}
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@book{einstein1956investigations,
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bibtex_show={true},
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title={Investigations on the Theory of the Brownian Movement},
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author={Einstein, Albert},
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year={1956},
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publisher={Courier Corporation},
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preview={brownian-motion.gif}
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}
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@article{einstein1950meaning,
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abbr={AJP},
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bibtex_show={true},
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title={The meaning of relativity},
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author={Einstein, Albert and Taub, AH},
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journal={American Journal of Physics},
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volume={18},
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number={6},
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pages={403--404},
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year={1950},
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publisher={American Association of Physics Teachers}
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}
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@article{PhysRev.47.777,
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abbr={PhysRev},
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title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
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author={Einstein*†, A. and Podolsky*, B. and Rosen*, N.},
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abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
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journal={Phys. Rev.},
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location={New Jersey},
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volume={47},
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issue={10},
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pages={777--780},
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numpages={0},
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year={1935},
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month={May},
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publisher=aps,
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doi={10.1103/PhysRev.47.777},
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url={http://link.aps.org/doi/10.1103/PhysRev.47.777},
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html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777},
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pdf={example_pdf.pdf},
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altmetric={248277},
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dimensions={true},
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google_scholar_id={qyhmnyLat1gC},
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video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ},
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additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)},
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annotation={* Example use of superscripts<br>† Albert Einstein},
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@article{archit2025segment,
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title={Segment anything for microscopy},
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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},
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journal={Nature Methods},
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volume={22},
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number={3},
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pages={579--591},
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year={2025},
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publisher={Nature Publishing Group US New York},
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doi={https://doi.org/10.1038/s41592-025-02745-9},
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preview={micro-sam.png},
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selected={true},
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inspirehep_id = {3255}
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}
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@article{einstein1905molekularkinetischen,
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title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen},
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author={Einstein, A.},
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journal={Annalen der physik},
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volume={322},
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number={8},
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pages={549--560},
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year={1905},
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publisher={Wiley Online Library}
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@article{muth2025synapsenet,
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title={SynapseNet: deep learning for automatic synapse reconstruction},
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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},
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journal={Molecular Biology of the Cell},
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volume={36},
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number={10},
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pages={ar127},
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year={2025},
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publisher={The American Society for Cell Biology},
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doi={https://doi.org/10.1091/mbc.E24-11-0519},
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selected={true}
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}
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@article{einstein1905movement,
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abbr={Ann. Phys.},
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title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat},
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author={Einstein, A.},
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journal={Ann. Phys.},
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volume={17},
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pages={549--560},
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year={1905}
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@misc{griebel2025segmenthistopathology,
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title={Segment Anything for Histopathology},
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author={Titus Griebel and Anwai Archit and Constantin Pape},
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year={2025},
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eprint={2502.00408},
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archivePrefix={arXiv},
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primaryClass={eess.IV},
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url={https://arxiv.org/abs/2502.00408},
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}
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@article{einstein1905electrodynamics,
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title={On the electrodynamics of moving bodies},
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author={Einstein, A.},
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year={1905}
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@misc{teuber2025parameterefficientfinetuningsegment,
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title={Parameter Efficient Fine-Tuning of Segment Anything Model for Biomedical Imaging},
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author={Carolin Teuber and Anwai Archit and Constantin Pape},
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year={2025},
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eprint={2502.00418},
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archivePrefix={arXiv},
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primaryClass={cs.CV},
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url={https://arxiv.org/abs/2502.00418},
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}
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@Article{einstein1905photoelectriceffect,
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bibtex_show={true},
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abbr={Ann. Phys.},
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title="{{\"U}ber einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt}",
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author={Albert Einstein},
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abstract={This is the abstract text.},
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journal={Ann. Phys.},
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volume={322},
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number={6},
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pages={132--148},
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year={1905},
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doi={10.1002/andp.19053220607},
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award={Albert Einstein receveid the **Nobel Prize in Physics** 1921 *for his services to Theoretical Physics, and especially for his discovery of the law of the photoelectric effect*},
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award_name={Nobel Prize}
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@article{JeremiasPape+2025+203+213,
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url = {https://doi.org/10.1515/mim-2024-0021},
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title = {Stamped counting for biomedical images},
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author = {Julia Jeremias and Constantin Pape},
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pages = {203--213},
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volume = {2},
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number = {2},
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journal = {Methods in Microscopy},
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doi = {doi:10.1515/mim-2024-0021},
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year = {2025},
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lastchecked = {2025-10-10}
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}
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@book{przibram1967letters,
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bibtex_show={true},
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title={Letters on wave mechanics},
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author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl},
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year={1967},
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publisher={Vision},
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preview={wave-mechanics.gif},
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abbr={Vision}
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@misc{archit2025probabilisticdomainadaptationbiomedical,
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title={Probabilistic Domain Adaptation for Biomedical Image Segmentation},
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author={Anwai Archit and Constantin Pape},
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year={2025},
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eprint={2303.11790},
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archivePrefix={arXiv},
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primaryClass={cs.CV},
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url={https://arxiv.org/abs/2303.11790},
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}
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_config.yml

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# Site settings
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# -----------------------------------------------------------------------------
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title: blank # the website title (if blank, full name will be used instead)
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first_name: You
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middle_name: R.
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last_name: Name
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title: Computational Cell Analytics # the website title (if blank, full name will be used instead)
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first_name: Marei
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middle_name:
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last_name:
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contact_note: >
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You can even add a little note about which of these is the best way to reach you.
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Reach out best via mail.
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description: > # the ">" symbol means to ignore newlines until "footer_text:"
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A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design.
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footer_text: >
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- lighthouse_results/
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- package.json
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- package-lock.json
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- _pages/about_einstein.md
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- _pages/blog.md
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- _pages/dropdown.md
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- purgecss.config.js
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- README.md
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# MAKE SURE imagemagick is installed and on your PATH before enabling imagemagick. In a terminal, run:
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# convert -version
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imagemagick:
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enabled: true # enables responsive images for your site (recommended, see https://github.com/alshedivat/al-folio/issues/537)
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enabled: false # enables responsive images for your site (recommended, see https://github.com/alshedivat/al-folio/issues/537)
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widths:
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_data/repositories.yml

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github_users:
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- torvalds
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- alshedivat
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# github_users:
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repo_description_lines_max: 2
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github_repos:
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- alshedivat/al-folio
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- jekyll/jekyll
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- twbs/bootstrap
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- jquery/jquery
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- FortAwesome/Font-Awesome
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- mathjax/MathJax
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- jpswalsh/academicons
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- computational-cell-analytics/computational-cell-analytics
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- computational-cell-analytics/micro-sam
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- computational-cell-analytics/dl-for-micro
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- computational-cell-analytics/synapse-net

_data/socials.yml

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# bluesky_url: # your bluesky URL
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# dblp_url: # your DBLP profile url
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# discord_id: # your discord id (18-digit unique numerical identifier)
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email: [email protected] # your email address
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email: [email protected] # your email address
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# facebook_id: # your facebook id
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# flickr_id: # your flickr id
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# github_username: # your GitHub user name
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github_username: computational-cell-analytics # your GitHub user name
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# gitlab_username: # your GitLab user name
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# hal_id: # your HAL id (https://hal.science/)
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# ieee_id: # your ieeexplore.ieee.org/author/id
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inspirehep_id: 1010907 # Inspire HEP author ID
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# inspirehep_id: 1010907 # Inspire HEP author ID
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# instagram_id: # your instagram id
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# kaggle_id: # your kaggle id
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# keybase_username: # your keybase user name
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# publons_id: # your ID on Publons
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# quora_username: # your Quora username
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# research_gate_profile: # your profile on ResearchGate
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rss_icon: true # comment this line to hide the RSS icon
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scholar_userid: qc6CJjYAAAAJ # your Google Scholar ID
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# rss_icon: true # comment this line to hide the RSS icon
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# scholar_userid: qc6CJjYAAAAJ # your Google Scholar ID
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# scopus_id: # your profile on Scopus
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# semanticscholar_id: # your Semantic Scholar ID
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# spotify_id: # your spotify id
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# x_username: # your X handle
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# youtube_id: # your youtube channel id (youtube.com/@<youtube_id>)
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# zotero_username: # your zotero username
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custom_social: # can be any name here other than the ones already defined above
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logo: https://www.alberteinstein.com/wp-content/uploads/2024/03/cropped-favicon-192x192.png # can be png, svg, jpg
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title: Custom Social
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url: https://www.alberteinstein.com/
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# custom_social: # can be any name here other than the ones already defined above
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# logo: https://www.alberteinstein.com/wp-content/uploads/2024/03/cropped-favicon-192x192.png # can be png, svg, jpg
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# title: Custom Social
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# url: https://www.alberteinstein.com/

_news/announcement_3.md

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---
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layout: post
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date: 2016-01-15 07:59:00-0400
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date: 2025-10-8 07:59:00-0400
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inline: true
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related_posts: false
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---
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A simple inline announcement with Markdown emoji! :sparkles: :smile:
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This website was created! :sparkles:

_pages/about.md

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layout: about
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title: about
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permalink: /
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subtitle: <a href='#'>Affiliations</a>. Address. Contacts. Motto. Etc.
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subtitle: <a href='#'>Institute of Computer Science</a> Georg-August University Göttingen
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profile:
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image: prof_pic.jpg
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image: group_picture.jpg
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image_circular: false # crops the image to make it circular
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more_info: >
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<p>555 your office number</p>
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<p>123 your address street</p>
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<p>Your City, State 12345</p>
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# more_info: >
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# <p>555 your office number</p>
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# <p>123 your address street</p>
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# <p>Your City, State 12345</p>
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selected_papers: true # includes a list of papers marked as "selected={true}"
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social: true # includes social icons at the bottom of the page
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limit: 5 # leave blank to include all the news in the `_news` folder
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latest_posts:
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enabled: true
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enabled: false
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scrollable: true # adds a vertical scroll bar if there are more than 3 new posts items
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limit: 3 # leave blank to include all the blog posts
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---
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Write your biography here. Tell the world about yourself. Link to your favorite [subreddit](http://reddit.com). You can put a picture in, too. The code is already in, just name your picture `prof_pic.jpg` and put it in the `img/` folder.
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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.
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Put your address / P.O. box / other info right below your picture. You can also disable any of these elements by editing `profile` property of the YAML header of your `_pages/about.md`. Edit `_bibliography/papers.bib` and Jekyll will render your [publications page](/al-folio/publications/) automatically.
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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.
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Link to your social media connections, too. This theme is set up to use [Font Awesome icons](https://fontawesome.com/) and [Academicons](https://jpswalsh.github.io/academicons/), like the ones below. Add your Facebook, Twitter, LinkedIn, Google Scholar, or just disable all of them.
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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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<!-- Link to your social media connections, too. This theme is set up to use [Font Awesome icons](https://fontawesome.com/) and [Academicons](https://jpswalsh.github.io/academicons/), like the ones below. Add your Facebook, Twitter, LinkedIn, Google Scholar, or just disable all of them. -->

_pages/about/anwai.md

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**Anwai Archit** \
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PhD student

_pages/about/caro.md

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**Carolin Teuber** \
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PhD Student

_pages/about/constantin.md

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**Constantin Pape**\
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Group leader

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