Image Analysis
| Citation | Link | Keywords |
| Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021). | https://www.nature.com/articles/s41592-020-01018-x | Segmentation, Tools, Deep Learning |
| Ershov, D., Phan, MS., Pylvänäinen, J.W. et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods 19, 829–832 (2022). | https://www.nature.com/articles/s41592-022-01507-1 | Tracking, Tools |
| Archit, A., Freckmann, L., Nair, S. et al. Segment Anything for Microscopy. Nat Methods 22, 579–591 (2025). | https://www.nature.com/articles/s41592-024-02580-4 | Segmentation, Tools, Deep Learning |
| van Ooijen, Hanna et al.
A thermoplastic chip for 2D and 3D correlative assays combining screening and high-resolution imaging of immune cell responses. Cell Reports Methods, Volume 5, Issue 1, 100965 |
https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(25)00001-3 |
imaging, microwell, correlative imaging, high-resolution, tumor microenvironment, natural killer cell |
Bray, Mark-Anthony, et al. "Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes." Nature protocols 11.9 (2016): 1757-1774.
https://www.nature.com/articles/nprot.2016.105
segmentation, data analysis, image based biology
Gerst, Ruman, Zoltán Cseresnyés, and Marc Thilo Figge. "JIPipe: visual batch processing for ImageJ." nature methods 20.2 (2023): 168-169.
bioimage analysis tool
Schindelin, Johannes, et al. "Fiji: an open-source platform for biological-image analysis." Nature methods 9.7 (2012): 676-682.
bioimage analysis tool
Carpenter, Anne E., et al. "CellProfiler: image analysis software for identifying and quantifying cell phenotypes." Genome biology 7.10 (2006): R100.
bioimage analysis tool
Dosovitskiy, Alexey. "An image is worth 16x16 words: Transformers for image recognition at scale." arXiv preprint arXiv:2010.11929 (2020).
Deep Learning