Doumane M, Lionnet C, Bayle V, Jaillais Y, Caillaud MC#. Automated Tracking of Root for Confocal Time-lapse Imaging of Cellular Processes. Bio Protoc. 2017 Apr 20;7(8). pii: e2245. doi: 10.21769/BioProtoc.2245. PMID: 28459086

Automatic quantification of the number of intracellular compartments in Arabidopsis thaliana root cells

Sice spot detector macro for ImageJ (SiCE SpotDetector.ijm)

Wavelet A Trou plug-in for ImageJ (Wavelet_A_Trou.jar)

For testing the macro you can download image examples here

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Bayle V, Platre MP, Jaillais Y#. Automatic Quantification of the Number of Intracellular Compartments in Arabidopsis thaliana Root Cells. Bio Protoc. 2017 Feb 20;7(4). pii: e2145. doi: 10.21769/BioProtoc.2145.

Automated tracking of root for confocal time-lapse imaging of cytokinesis

You can download the three files required for automated tracking of roots here:  Files_BioProtocol_Doumane.zip.

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Platre MP, Jaillais Y. " Exogenous treatment of Arabidopsis seedlings with lyso-phospholipids for the inducible complementation of lipid mutants". STAR Protoc. 2 1-13 (2021) PMID : 34223200

https://star-protocols.cell.com/protocols/749

https://github.com/mplatre/Macro_Rosette_Size/releases/tag/V1

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Bayle V*, Fiche JB*, Burny C, Platre MP, Nollmann MP, Martinière A# and Jaillais Y#. Single-particle tracking Photo-Activated Localization Microscopy of membrane proteins in living plant tissues. Nature protocols. 1600–1628 (2021). https://doi.org/10.1038/s41596-020-00471-4

●  sptPALM_viewer code is available on GitHub (https://github.com/jbfiche/sptPALM_cbs), and astandalone application is freely available here: (http://bioserv.cbs.cnrs.fr/DOWNLOAD/sptPALM_data/ in the Softwares.zip file)

● MTT (http://www.ciml.univ-mrs.fr/fr/technologie/imagimm/softwares) or TrackMate (https://imagej.net/TrackMate)

●  Stack_Split_macro.ijm (http://bioserv.cbs.cnrs.fr/DOWNLOAD/sptPALM_data/ in the Softwares.zip file)

●  SPTpalm_Rscript.R R script (http://bioserv.cbs.cnrs.fr/DOWNLOAD/sptPALM_data/ in the
Softwares.zip file)