blender-tissue-cartography 0.0.4

Pipeline for tissue extraction and analysis of surfaces from volumetric mircroscopy data using blender

blender-tissue-cartography

What this tool does

Tissue cartography extracts and cartographically projects curved surfaces from volumetric image data. This turns your 3d data into 2d data which is much easier to visualize, analyze, and computationally process. Tissue cartography is particularly useful in developmental biology, analyzing 3d microscopy data by taking advantage of the laminar, sheet-like organization of many biological tissues. For more on tissue cartography, see our methods paper, Heemskerk & Streichan 2015 and Mitchell & Cislo 2023.

blender_tissue_cartography comprises an add-on to do tissue cartography using the popular 3d creation software blender, a python library for creating custom/automatized analysis pipelines, and a set of template analysis pipelines/tutorials.

Work in progress!

This project is a work in progress and may change rapidly. Please update regularly.

Installation

blender_tissue_cartography comprises both a Blender add-on and a python library.

• The add-on does tissue cartography 100% within the Blender graphical user interface. Use the add-on if you quickly want to process a new dataset, or if you are not a coding expert.

• The python library allows expert users to develop custom or automatized pipelines.

System requirements Both the Python library and the add-on have no minimum system requirements and can run on any modern laptop. For processing volumetric image data, you will need sufficient RAM (at least ~4x of the size of the volumetric data, e.g. 8GB RAM dfor a 2GB volumetric .tif file). Blender will run much faster if your computer has a GPU. The MeshLab library which is required for some (non-essential) operations is not available of new ARM Apple computers.

Blender add-on

1. Install the non-python programs: Blender 4.3 (pre-4.3 version will not work) and Ilastik. You do not need to install python or any python libraries.

   • Optionally, install Fiji (for looking at 3D .tifs) and Meshlab (for advanced surface extraction and remeshing)

2. From GitHub, download the file blender_addon/blender_tissue_cartography-1.0.0-[XXX].zip where [XXX] is your operating system (e.g. linux_x64). You do not need to unpacl the .zip.

   • If your operating system is not available, you can also download blender_addon/blender_tissue_cartography.py. In this case you will need to install the python library scikit-image in Blender’s Python interface.

3. Install the add-on: Click “Edit -> Preferences -> Add-ons -> Add-on Settings -> Install from disk” and select the .zip file you just downloaded (you don’t need to unpack it).

4. Restart Blender. The add-on can now be found under “Scene -> Tissue Cartography”.

Python library

1. Install the non-python programs: Fiji (optional), Ilastik, Meshlab (optional), and Blender.

2. Install Python via anaconda/miniconda, if you haven’t already.

3. Install blender_tissue_cartography: run pip install blender-tissue-cartography in a command window.

4. (Optional) Install extra Python library for pymeshlab, required for some advanced (re)meshing functionality. This package is not available on new ARM Apple computers.

   • run pip install pymeshlab in a command window

The project is hosted on pip, with source code on GitHub.

Developer installation

If you want to extend blender_tissue_cartography:

1. Clone the github repository.

2. Create a conda environment with all Python dependencies and install the blender_tissue_cartography module. Open a command window in the blender-tissue-cartography directory and type:

   • conda env create -n blender_tissue_cartography -f environment.yml
   • conda activate blender_tissue_cartography
   • pip install -e .

3. (Optional) Install extra Python library for pymeshlab, required for some advanced functionality (remeshing and surface reconstruction from within Python).

   • pip install pymeshlab - Note that this package is not available on new ARM Apple computers.

4. Install nbdev

Known issues

• When using the add-on, please save your .blend project to disk before using any of the add-on functionality. Otherwise, Blender may crash.

• 3D .tif files loaded into Blender are not saved to the .blend (which would explode in size). If you close Blender, you need to reimport your 3D image data.

• Please report any issues or bugs you find on GitHub!

Documentation

• Documentation webpage

• Datasets and interactive Jupyter notebooks for the tutorials can be downloaded from GitHub

• The methods paper explains the general idea of tissue cartography, the design of blender_tissue_cartography, and shows several examples.

Basic usage

For a complete set of tutorials, see the documentation website.

Tissue cartography workflow

Tissue cartography starts with a 3D, volumetric image.

1. Create a segmentation of your 3D data to identify the surface you want to extract

2. Convert the segmentation into a mesh of your surface of interest

3. Cartographically unwrap the mesh into a 2D plane

4. Project your 3D data onto the unwrapped mesh

5. Visualize the results in 3D using blender or use the 2D projected data for quantitative analysis.

6. Batch process multiple 3D images (e.g. frames of a movie)

Blender add-on

The Blender add-on allows you to carry out steps 2-5 entirely within Blender. Here is a screenshot using the example Drosophila dataset:

Left: Projected 2D image. Center: 3D view of image data (volume bounding box, image slices, and extracted surface). Right: Tissue Cartography add-on panel.

In Blender, you can edit meshes and cartographic projections interactively - you can create a preliminary projection of your data automatically, and use it as guidance when editing your cartographic map in blender. Here, we edit the “seam” of our cartographic map based on the region occupied by cells during zebrafish epiboly (tutorial 6).

Dynamic datasets

blender_tissue_cartography also allows creating cartographic projections of dynamic datasets (i.e. movies), where the surface of interest can move or deform over time. The user creates a cartographic projection for a reference timepoint which is transfered to all other time-points using surface-to-surface registration algorithms. This generates consistent projections across all timepoints - see tuorials 8 and 9.

Python library

For advanced users, the blender_tissue_cartography library allows creating custom and automated tissue cartography pipelines, typically run from a jupyter computational notebook (which can also serve as lab notebook - notes, comments on the data). blender_tissue_cartography also provides tools for correct quantitative analysis of image data on curved surfaces.

Below is a screenshot to give you an idea of the workflow for the example Drosophila dataset: Volumetric data in ImageJ (center), jupyter computational notebook to run the blender_tissue_cartography module (left), and blender project with extracted mesh and texture (right).

Tutorials

Fully worked-out tutoruals are provided on the documentation webpage. Test data for the tutorials can be downloaded from the nbs/Tutorials/ directory.

For the Python library, tutorials take the form of jupyter computational notebooks which you can download and run on your own computer (click the green button “Code” to download a .zip.) To run a tutorial on your computer, follow the installation instructions and then launch jupyter and work through the notebooks in the Tutorials directory in order. I recommended being comfortable with running simple Python code (you don’t have to do any coding yourself).

The tutorial notebooks can be used as templates for your own analysis pipelines. Here is an example of a jupyter computational notebook (left), and the created projection visualized in Blender (right).

Notes for Python beginners

• You will need a working Python installation (see here: installing anaconda/miniconda, and know how to launch jupyter notebooks. You will run the computational notebooks in your browser. Here is a video tutorial

• Create a new folder for each tissue cartography project. Do not place them into the folder into which you unpacked blender_tissue_cartography - otherwise, your files will be overwritten if you want to update the software

• The repository contains two sets of notebooks: in the nbs folder and in the nbs/Tutorials folder. The nbs-notebooks are for developing the code. If you don’t want to develop/adapt the code to your needs, you don’t need to look at them. Copy a notebook from the nbs/Tutorials folder - e.g. 03_basics_example.ipynb - into your project folder to use it as a template.

• You do not need to copy functions into your notebooks manually. If you follow the installation instructions, the code will be installed as a Python package and can be “imported” by Python. See tutorials!

Software stack

Note: the Python libraries will be installed automatically if you follow the installation instructions above.

Required

• Python, with the following libraries
  • jupyter
  • numpy / Matplotlib / Scipy
  • skimage various image processing tools.
  • h5py for reading/writing of .h5 files.
  • tifffile for reading/writing of .tif files, including metadata.
  • libigl Geometry processing.
• Ilastik Image classification and segmentation,
• Blender Mesh editing and UV mapping.

Optional

• Meshlab GUI and Python library with advanced surface reconstruction tools (required for some workflows).

• Python libraries:

  • PyMeshLab Python interface to MeshLab.
  • nbdev for notebook-based development, if you want to add your own code

Other useful software

• MicroscopyNodes plug-in for rendering volumetric .tif files in blender
• Boundary First Flattening advanced tool for creating UV maps with graphical and command line interface
• pyFM python library for mesh-to-mesh registration (for dynamic data) which may complement the algorithms that ship with blender_tissue-cartography

Acknowledgements

This software is being developed by Nikolas Claussen in the Streichan lab at UCSB. We thank Cecile Regis, Susan Wopat, Noah Mitchell, An Yan, Pieter Derksen, Matthew Lefebvre, Sean Komura, Gary Han, Boris Fosso, and Dillon Cislo, for sharing data, advice, and software testing.

Citation

If you use blender_tissue_cartography for your work, please cite:

Nikolas Claussen, Cécile Regis, Susan Wopat, and Sebastian Streichan: Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data. bioRxiv 2025.02.04.636523; doi: https://doi.org/10.1101/2025.02.04.636523