The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines
Open accessAbstract
TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitatively and quantitatively that these new capabilities function effectively across a wide range of bio-imaging experiments. TrackMate 7 combines the benefits of machine and deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.
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Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890
Cellpose: a generalist algorithm for cellular segmentation
Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021) · Nature Methods · doi:10.1038/s41592-020-01018-x · Cited by 4,369
TrackMate: An open and extensible platform for single-particle tracking
Tinevez, J.-Y., Perry, N., Schindelin, J., Hoopes, G. M., Reynolds, G. D., Laplantine, E., Bednarek, S. Y., Shorte, S. L., & Eliceiri, K. W. (2017) · Methods · doi:10.1016/j.ymeth.2016.09.016 · Cited by 3,380
Self-citationilastik: interactive machine learning for (bio)image analysis
Berg, S., Kutra, D., Kroeger, T., Straehle, C. N., Kausler, B. X., Haubold, C., Schiegg, M., Ales, J., Beier, T., Rudy, M., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0582-9 · Cited by 3,368
Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
Arganda-Carreras, I., Kaynig, V., Rueden, C., Eliceiri, K. W., Schindelin, J., Cardona, A., & Sebastian Seung, H. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx180 · Cited by 2,424
Cell Detection with Star-Convex Polygons
Schmidt, U., Weigert, M., Broaddus, C., & Myers, G. (2018) · Lecture Notes in Computer Science · doi:10.1007/978-3-030-00934-2_30 · Cited by 1,826
CellProfiler 3.0: Next-generation image processing for biology
McQuin, C., Goodman, A., Chernyshev, V., Kamentsky, L., Cimini, B. A., Karhohs, K. W., Doan, M., Ding, L., Rafelski, S. M., Thirstrup, D., et al. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2005970 · Cited by 1,825
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ
Legland, D., Arganda-Carreras, I., & Andrey, P. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw413 · Cited by 1,393
Feature point tracking and trajectory analysis for video imaging in cell biology
Sbalzarini, I. F., & Koumoutsakos, P. (2005) · Journal of Structural Biology · doi:10.1016/j.jsb.2005.06.002 · Cited by 1,392
Deep learning for cellular image analysis
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Jelli, E., Ohmura, T., Netter, N., Abt, M., Jiménez‐Siebert, E., Neuhaus, K., Rode, D. K. H., Nadell, C. D., & Drescher, K. (2023) · Molecular Microbiology · doi:10.1111/mmi.15064 · Cited by 48
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Self-citationMantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells
Ivanov, I. E., Hirata-Miyasaki, E., Chandler, T., Cheloor-Kovilakam, R., Liu, Z., Pradeep, S., Liu, C., Bhave, M., Khadka, S., Arias, C., et al. (2024) · PNAS Nexus · doi:10.1093/pnasnexus/pgae323 · Cited by 21
Metadata
- Authors
- Ershov, D., Phan, M.-S., Pylvänäinen, J. W., Rigaud, S. U., Le Blanc, L., Charles-Orszag, A., Conway, J. R. W., Laine, R. F., Roy, N. H., Bonazzi, D., Duménil, G., Jacquemet, G., & Tinevez, J.-Y.
- Venue
- Nature Methods
- Published
- 2022-06-02
- Volume
- 19
- Issue
- 7
- Pages
- 829-832
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W4281665512
- Cited by
- 1,201
- References
- 32
- FWCI
- 90.01
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Ershov, D., Phan, M.-S., Pylvänäinen, J. W., Rigaud, S. U., Le Blanc, L., Charles-Orszag, A., Conway, J. R. W., Laine, R. F., Roy, N. H., Bonazzi, D., Duménil, G., Jacquemet, G., & Tinevez, J.-Y. (2022). TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nature Methods. https://doi.org/10.1038/s41592-022-01507-1
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