Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data

Tissue cartography extracts and cartographically projects surfaces from volumetric biological image data. This turns 3D-into 2D data which is much easier to visualize, analyze, and computationally process. Tissue cartography has proven particularly useful in developmental biology by taking advantage of the sheet-like organization of many biological tissues. However, existing software tools for tissue cartography are limited in the type of geometries they can handle and difficult for non-experts to use and extend. Here, we describe<monospace><ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://nikolas-claussen.github.io/blender-tissue-cartography/">blender_tissue_cartography</ext-link></monospace>(<monospace>btc</monospace>), a tissue cartography add-on for the popular 3D creation software Blender.<monospace>btc</monospace>makes tissue cartography user-friendly via a graphical user interface and harnesses powerful algorithms from the computer graphics community for biological image analysis. The<monospace>btc</monospace>GUI enables interactive analysis and visualization without requiring any programming expertise, while an accompanying Python library allows expert users to create custom analysis pipelines. Both the add-on and the Python library are highly modular and fully documented, including interactive Jupyter Notebook tutorials.<monospace>btc</monospace>features a general-purpose pipeline for time-lapse data in which the user graphically defines a cartographic projection for a singlekey frame, which is propagated to all other frames via surface-to-surface alignment algorithms. The<monospace>btc</monospace>differential geometry module allows mathematically correcting for cartographic distortion, enabling faithful 3D measurements in 2D cartographic projections, including for vector fields like tissue flow fields. We demonstrate<monospace>btc</monospace>on diverse and complex tissue shapes fromDrosophila, stem-cell-based organoids,Arabidopsis, and zebrafish.