---
# System prepended metadata

title: BioMedPhys Group Meeting

---

## 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.
