## Biomedical Physics </br>
# Group Seminar and Journal Club

* Wednesday, __13:00__, every week
* hybrid in room 25.23/01.34 and online via WebEx:
* https://hhu.webex.com/meet/philip
* alternating **presentations** and **journal club**

## Schedule for Summer Semester 2025

Please swap slots with someone else if you cannot make it.

| Date | Event | Presenter | Topic |
| -------- | -------- | -------- | -------- |
| May 07 | Journal Club | | |
| May 14 | Group Meeting | Lucas | Progress Report |
| May 21 | Journal Club | | |
| May 28 | _no meeting_ | ---- | ---- |
| Jun 04 | _no meeting_ | ---- | ---- |
| Jun 11 | Group Meeting | Felix | Progress Report |
| Jun 18 | | | |
| Jun 25 | | | |
| Jul 02 | Group Meeting | Lennard | Progress Report |
| Jul 09 | Group Meeting | Kristopher | Progress Report |
| Jul 16 | | | |

----

## Old Schedule for Winter Semester 2024/25

| Date | Event | Presenter | Topic |
| -------- | -------- | -------- | -------- |
| Oct 16 | Group Meeting | Diana | Progress Report |
| Oct 23 | Journal Club | Philip / all | DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning <br/> https://www.nature.com/articles/s41592-023-01966-0 |
| Oct 30 | ---- | ---- | ---- |
| Nov 06 | Group Meeting | Tristan Beste<br>(Helmholtz Center, Würzburg) | Guest Speaker |
| Nov 13 | Group Meeting | Rick Seifert<br>(Biotechnology & Biophysics, Uni Würzburg) | Guest Speaker |
| Nov 20 | Group Meeting | Luisa Coen (Exp. Med. Physik HHU) | Guest Speaker |
| Nov 27 | ---- | ---- | ---- |
| Dec 4 | Group Meeting | Lennard | Progress Report |
| Dec 11 | Group Meeting | Felix | Progress Report |
| Dec 18 | Journal Club | | |
| Jan 15 | Group Meeting | Lucas | Progress Report |
| Jan 22 | Journal Club | t.b.a. | |
| ~~Jan 29~~<br>Feb 05</br>| Group Meeting | Maxime Gorres | De-Wedging of Electron Tomograms |

## Old Schedule for Summer Semester 2024

| Date | Event | Presenter | Topic |
| -------- | -------- | -------- | -------- |
| Apr 10 | Safety Instructions | Philip | Lab Safety |
| Apr 17 | Group Meeting | Diana | TAC test talk |
| Apr 24 | Journal Club | Philip | https://www.nature.com/articles/s41592-024-02233-6 (MEDIAR, SegFormer, ConvNext etc.) |
| May 1 | -- | -- | -- |
| May 8 | -- | -- | -- |
| May 15 | Group Meeting | Lucas | Progress report [links](https://docs.google.com/document/d/1oCHpwM-M7uXAKll-SK63ybyba3_lKNF8sHxqdPYCCIc/edit?usp=sharing)|
| May 22 | Journal Club | Philip/Maxime | Tomogram De-Wedging with Deep Learning:<br>https://www.nature.com/articles/s41467-022-33957-8 and https://arxiv.org/abs/2311.05539 |
| May 29 | Group Meeting | Lennard | Hybrid CPM-MD model |
| Jun 5 | Journal Club | Philip | (Latent) Diffusion Neural Networks:<br>https://arxiv.org/abs/2006.11239 and <br>https://arxiv.org/abs/2112.10752|
| Jun 12 | -- | -- | -- |
| Jun 19 | Group Meeting | Felix | Progress report |
| Jun 26 | -- | -- | -- |
| Jul 3 | Group Meeting | Simon Heckhausen | Dimension reduction for clinical flow cytometry data |
| Jul 10 | Group Meeting | Kristopher Nolte | Progress Report (Mosquito wing classification with deep learning) |

## Old Schedule (2022-2023)

| Date | Event | Presenter | Topic |
| -------- | -------- | -------- | -------- |
| **2022** | | | |
| Dec 07 | Group Meeting | all | 1st meeting at HHU - Introduction round |
| Dec 14 | Group Meeting | Rick | PhD Startup Meeting |
| Dec 22 (Thursday!) | Journal Club | Diana | de Vries et al. (**2022**): 3D single-cell shape analysis of cancer cells using geometric deep learning https://www.biorxiv.org/content/10.1101/2022.06.17.496550v1 |
| **2023** | | | |
| Jan 11 | Group Meeting | Philip/Lennard/Diana/all | HPC and Microscopy at HHU |
| Jan 18 | External Speaker | Kristopher Nolte | The ConVector Project |
| Jan 25 | Group Meeting | Lennard | Simulation of tissue growth using the Cellular Potts Model |
| Feb 1 | Journal Club | Helmut | He et al. (**2021**): Masked Autoencoders Are Scalable Vision Learners </br> https://arxiv.org/pdf/2111.06377v2.pdf |
| February | --- | no meetings | --- |
| March 1 | Journal Club | Philip | Mühlberg et al. (**2022**), https://www.biorxiv.org/content/10.1101/2022.10.28.514253v1 |
| March 8 | Group Meeting | Tristan | PhD project presentation |
| March 15 | Group Meeting | Nicole | DPG Poster | |
| March 22 | no meeting (exams) | --- | --- |
| March 29 | Group Meeting | Diana | Project update | | --- |
| April 5 | Journal Club | Sebastian | Attention is all you need </br> https://arxiv.org/abs/1706.03762 |
| April 19 | Group Meeting | Lennard | Results on live stain of Fibronectin |
| April 26 | Journal Club | Philip | New publications with our collaborators: https://www.science.org/doi/full/10.1126/sciadv.add9275 and https://www.biorxiv.org/content/10.1101/2023.03.06.530721v2.abstract |
| May 3 | --- | no meeting | --- |
| May 10 | --- | no meeting | Philip at Max Planck Retreat |
| May 17 | --- | no meeting | 11:30 PhD Defense Sebastian Reinhard |
| May 24 | Group Meeting | Felix | Interactive neuro-mechanical simulation of C.Elegans locomotive behaviour |
| May 31 | --- | no meeting | --- |
| June 7 | --- | no meeting | Tuesday 16:30 Antrittsvorlesung Philip |
| June 14 | Journal Club | Diana | SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis, https://www.biorxiv.org/content/10.1101/2023.05.10.540085v1 |
| June 21 | Group Meeting | Ghizlane, Malte | project updates |
| June 28 | --- | no meeting | --- |
| July 5 | Group Meeting | Christina Meinert | project update |
| July/August | --- | meeting break | --- |
| Oct 25 | Group Meeting | Lennard Fastabend | Motion tracking in growing tissues |
| Nov 01 | *no meeting* | --- | --- |
| Nov 08 | Journal Club | Philip | Unsupervised Segmentation - https://www.biorxiv.org/content/10.1101/2023.08.21.554208v1 |
| Nov 15 | Group Meeting | Felix Fink | Project Update (Interactive neuro-mechanical simulation) |
| Nov 22 | Journal Club | Philip | Unsupervised Segmentation Pt. II |
| Nov 29 | Group Meeting | Kristopher Nolte |Master Thesis presentation (& visit to HHU) |
| Dec 06 | Journal Club | Philip | Deep Learning on Point Clouds https://arxiv.org/abs/1808.00671 |
| Dec 13 | Group Meeting | Rick Seifert | Annual report PhD-Project (high throughput receptor quantification) |
| Dec 20 | Journal Club | Tristan & Philip | Cell membrane generation & segmentation https://www.biorxiv.org/content/10.1101/2023.11.08.566343v1 |
| **2024** | | | |
| Jan 10 | Group Meeting | Lucas & Philip | Progress Report / Test Talk |
| Jan 17 | *no meeting* | --- | PoP Meeting |
| Jan 24 | Journal Club | Helmut & Philip | Unsupervised DL Denoising </br> https://arxiv.org/abs/2303.13132 + others|
| Jan 31 | Group Meeting | Tristan Beste | 3D Spatial Transcriptomics (Progress) |

## Possible papers for Journal Club

Look also here: https://www.zotero.org/groups/4563609/biomedphys-hhu-library/library

- Kirillov et al. “Segment Anything.” arXiv, April 5, 2023. https://doi.org/10.48550/arXiv.2304.02643.
- Bevilacqua et al. “High-Resolution Line-Scan Brillouin Microscopy for Live Imaging of Mechanical Properties during Embryo Development.” Nature Methods, March 30, 2023, 1–6. https://doi.org/10.1038/s41592-023-01822-1.
- Kumar et al., “Crossbill: An Open Access Single Objective Light-Sheet Microscopy Platform.” bioRxiv, May 1, 2021. https://doi.org/10.1101/2021.04.30.442190.
- Yang et al. “DaXi—High-Resolution, Large Imaging Volume and Multi-View Single-Objective Light-Sheet Microscopy.” Nature Methods 19, no. 4 (April 2022): 461–69. https://doi.org/10.1038/s41592-022-01417-2.
- Lappalainen et al., “Connectome-Constrained Deep Mechanistic Networks Predict Neural Responses across the Fly Visual System at Single-Neuron Resolution.” bioRxiv, March 13, 2023. https://doi.org/10.1101/2023.03.11.532232.
- Priessner et al., “Content-Aware Frame Interpolation (CAFI): Deep Learning-Based Temporal Super-Resolution for Fast Bioimaging,” November 3, 2021. https://doi.org/10.1101/2021.11.02.466664.
- Rens, Elisabeth G., and Leah Edelstein-Keshet. “From Energy to Cellular Forces in the Cellular Potts Model: An Algorithmic Approach.” PLOS Computational Biology 15, no. 12 (November 12, 2019): e1007459. https://doi.org/10.1371/journal.pcbi.1007459.