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Modern spatial microscopy has provided developmental biology with powerfulresearch tools. However, the recent significant technological breakthroughshave inevitably led to technical "bottlenecks" for the application of the newprocedures to other tasks. We have developed a protocol for the 3Dreconstruction of plant organelles and tissues from stacks of two-dimensionalimages obtained by means of a wide range of electron transmission and lightmicroscopy. This protocol can be applied to a large set of primary data: live,fixed or even paleobotanical material. For tissue reconstruction, we have alsodeveloped a protocol of cell lineage tracing based on the geometricalproperties of plant cells. For the tissue sample consisting of $n$ cells, thisapproach allows the reconstruction of up to $n-1$ cell divisions from theprevious cell generations. Our protocol complements the limitations of clonalanalysis and recent real-time approaches of lineage tracing. It works well inthe case of tissues with directed and non-directed growth. Using theseprotocols, the subcellular relations between the complex surface of plastidswith stromules and mitochondria in the tuber parenchyma cells in\textit{Corydalis bracteata} have been revealed. Moreover, for the embryo($n=17$) and the seedling shoot apex ($n=208$) of \textit{Calla palustris}, thecellular architecture and full cell genealogy of up to 15 cell generations havebeen reconstructed. Three relatively independent cell lineages with stem cellslocated at the surface of the shoot apex have been found. The possibility ofusing a wide range of software, including open-source projects, is discussed.

Reconstruction of the 3D structure and developmental history of plant cells and tissues