As promised here we have a collection of links and information
The Image.sc forum for all questions image analysis related Image.sc forum
The amazing QuPath documentation
Cellpose info
Gómez-de-Mariscal, E., Grobe, H., Pylvänäinen, J. W., Xénard, L., Henriques, R., Tinevez, J. Y., & Jacquemet, G. (2024). CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data. PLoS biology, 22(8), e3002740. https://doi.org/10.1371/journal.pbio.3002740
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, 19(7), 829–832. https://doi.org/10.1038/s41592-022-01507-1
Bankhead, P., Loughrey, M. B., Fernández, J. A., Dombrowski, Y., McArt, D. G., Dunne, P. D., McQuaid, S., Gray, R. T., Murray, L. J., Coleman, H. G., James, J. A., Salto-Tellez, M., & Hamilton, P. W. (2017). QuPath: Open source software for digital pathology image analysis. Scientific reports, 7(1), 16878. https://doi.org/10.1038/s41598-017-17204-5
von Chamier, L., Laine, R. F., Jukkala, J., Spahn, C., Krentzel, D., Nehme, E., Lerche, M., Hernández-Pérez, S., Mattila, P. K., Karinou, E., Holden, S., Solak, A. C., Krull, A., Buchholz, T. O., Jones, M. L., Royer, L. A., Leterrier, C., Shechtman, Y., Jug, F., Heilemann, M., … Henriques, R. (2021). Democratising deep learning for microscopy with ZeroCostDL4Mic. Nature communications, 12(1), 2276. https://doi.org/10.1038/s41467-021-22518-0
Loci - plugin to help create ground truth data for deep learning (ROI map command) LOCI plugins
Plug-in to measure the distribution of signal throughout a cell SpatialStatistics
Plug-in to measure distances DiAna
Helena Jambor's resources
Summary of the talk: From zero to figure hero: https://osf.io/preprints/osf/xgbyr
Blog https://helenajamborwrites.netlify.app/
- Severino Ribecca http://www.datavizcatalogue.com/
- Yan Holz https://python-graph-gallery.com/
- Ferdio http://datavizproject.com/
- Literature: Beyond bar and line plots: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002128
- cheatsheets for image prep for figures: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931257/
- community checklist for image publication: https://www.nature.com/articles/s41592-023-01987-9
- quantification of image quality in publications: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001161
Inspiring BMJ Infografics https://www.bmj.com/infographics
- Pick color schemes https://colorbrewer2.org
- Check if contrast of foreground and background are good https://webaim.org/resources/contrastchecker/
How to for Graphical Abstracts (without Biorender) https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011789
Pictogram resources:
- https://fontawesome.com/icons?d=gallery&c=animals USE WITH ATTRIBUTION, , neat: works on dekstop as font!
- The Nounproject. https://thenounproject.com/ USE WITH ATTRIBUTION Bild-PNG und Vektor-SVG die adaptiert werden kann, mit registrierung.
- Pictogram collection: https://www.svgrepo.com/
- https://www.flaticon.com/
- https://iconduck.com/
- https://simpleicons.org/ Biology/Science
- https://bioicons.com/
- http://phylopic.org/ --> Icons of all animals and plants etc
- General science: https://www.ebi.ac.uk/style-lab/general/fonts/v1.3/
- Science/chemistry icons: https://reactome.org/icon-lib
- SCIDRAW a repository of free SVG cartoons for science supported by the Sainsbury Wellcome Centre, CC-BY Medicine
- https://smart.servier.com/
- https://healthicons.org/