Protocols & methods:

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


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:


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


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).

  sptPALM_viewer code is available on GitHub (, and astandalone application is freely available here: ( in the file)

MTT ( or TrackMate (

  Stack_Split_macro.ijm ( in the file)

  SPTpalm_Rscript.R R script ( in the file)