img3 is a python package for image processing of large, 3D (volumetric) image data.

img3 is intended for:

• storing NumPy arrays in raw file format
• storing and reading image metadata from corresponding nrrd files, used in bio-imaging
• perform copmutations on image data

The img3D package is organized as follows:

• src : Source (C and Python) files.
• examples : Examples of simple use cases of the package.

• C compiler
• numpy

• C compiler with OpenMP support
• ImageJ
• Python packages: tifffile, numba, scipy.signal

cd src
make install

To customize the python interpreter, C compiler, and the compilation flags:

cd src
make install PY=python CC=clang CFLAGS_OPENMP= 'CFLAGS = -O2 -g'

Below are results from projects where img3D modules were used. A project-specific pipeline was developed to process and generate the quantification needed for each project. The rendering of the generated 3D segmentations was performed with Paraview.

A study for the efficacy of different drugs in neurodegenerative diseases. A novel image processing pipeline utilizing img3D modules was developed to quantify drug efficacy on the sub-cellular level, through object segmentation of stained neural cells in 3D whole mouse-brain scans.
The pipeline will be published together with the corresponding publication.

An international collaboration aiming to develop a new protein-based delivery system to the central nervous system of the brain. 3D images of whole mouse-brain scans were used to detect the bio-distribution of the delivery system, using light-sheet microscopy. Image processing was performed using a custom pipeline utilizing img3D modules.
Paper currently under review in Cell. The pipeline will be published together with the corresponding publication.

The package was developed in the labs of Prof. Petros Koumoutsakos (ETH Zurich) and Prof. Adriano Aguzzi (University of Zurich) by

• Sergey Litvinov
• Athena Economides
• Francesca Catto