PCA Imaging Workshop Webinar Series: introduction to 3D image analysis with MorphoGraphX

This webinar is the second in a series organized by the Plant Cell Atlas (PCA). It introduces basic functions in MorphoGraphX, an open-source software platform for 3D image analysis in biological applications.

MorphoGraphX is free and open source. Downloads for Linux and Windows are available here: https://morphographx.org/software/

This zenodo page contains datasets accompanying the webinar demonstrations, which is organized in two sections:

1) Analyzing 3D images in MorphoGraphX: the 2.5D approachDemonstration by Dr. Anne-Lise Routier-Kierzkowska (Université de Montréal). We use a dataset of confocal images and segmented meshes of the tomato shoot apical meristem (Kierzkowski et al. 2012, Barbier de Reuille et al. 2015).

Download the file Kierzkowski_2012_Tomato_meristem_3_timepoints.tar and extract the archive*.

2) Basics of 3D cell segmentation in MorphoGraphXDemonstration by Dr. Amélie Bauer. We will use unpublished confocal image datasets and segmented meshes from Dr. Amélie Bauer, generated in the lab of Daniel Kierzkowski (Université de Montréal) and provided here as training material accompanying the webinar. Please contact [e-mail] regarding permission for uses of this material beyond the scope of this webinar.

Download the file Bauer_3D_segmentation_unpublished.tar and extract the archive*.

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*help to extract the .tar archives: 

- Windows : Right-click the .tar or .tar.gz file and select "7-Zip" > "Extract Here".- Linux: in Command terminal, tar -xvf archive.tar