  Modern spatial microscopy has provided developmental biology with powerful
research tools. However, the recent significant technological breakthroughs
have inevitably led to technical "bottlenecks" for the application of the new
procedures to other tasks. We have developed a protocol for the 3D
reconstruction of plant organelles and tissues from stacks of two-dimensional
images obtained by means of a wide range of electron transmission and light
microscopy. This protocol can be applied to a large set of primary data: live,
fixed or even paleobotanical material. For tissue reconstruction, we have also
developed a protocol of cell lineage tracing based on the geometrical
properties of plant cells. For the tissue sample consisting of $n$ cells, this
approach allows the reconstruction of up to $n-1$ cell divisions from the
previous cell generations. Our protocol complements the limitations of clonal
analysis and recent real-time approaches of lineage tracing. It works well in
the case of tissues with directed and non-directed growth. Using these
protocols, the subcellular relations between the complex surface of plastids
with 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}, the
cellular architecture and full cell genealogy of up to 15 cell generations have
been reconstructed. Three relatively independent cell lineages with stem cells
located at the surface of the shoot apex have been found. The possibility of
using a wide range of software, including open-source projects, is discussed.
