This repository contains the software to run a self-driving, multi-scale microscope and tools to process and analyse the resulting data.
Contains code to determine the curvature of macrophages from the high-resolution data.
Contains code to calculate the Hopkins statistics based on the low-resolution data.
Contains code to run the morphological feature analysis of the high-resolution macrophages.
Contains code to run a self-driving, multi-scale light-sheet microscope, including the context_driven_env.yml environment file.
Contains code to run our high-resolution macrophage segmentation pipeline using connected component labeling and a Cellpose-based 3D segmentation pipeline. The environmen is available as .yml file.
Contains code to run our low-resolution macrophage segmentation pipeline based on CLIJ, including a .yml environment file.
Contains code to stitch 3D data using translation based on the stage positions using Fast Fourier transform-based cross-correlations on the overlapping sections.
Contains code to visualize time-lapse data using ImageJ (generatelabel_colormap.ijm) and Napari (low- and high-res data).