This repository contains the software to analyze data from a self-driving, multi-scale microscope and tools to process and analyse the resulting data.
A preprint about this work is available: https://www.biorxiv.org/content/10.1101/2024.02.28.582579v1
and detailed documentation with instructions on how to run the code is available here: https://daetwylerstephan.github.io/multi-scale-image-analysis/
including links to testdata sets and parameters.
As a quick overview:
Contains code to determine the curvature of cells such as macrophages from the high-resolution data, including a compiled Matlab runtime version.
Contains code to run the morphological feature analysis of cells in the high-resolution data, including a compiled Matlab runtime version.
Contains code to calculate the Hopkins statistics based on the low-resolution cell position data, including a compiled Matlab runtime version.
Contains code to run our high-resolution macrophage segmentation pipeline using connected component labeling and a Cellpose-based 3D segmentation pipeline.
Contains code to run our low-resolution macrophage segmentation pipeline based on CLIJ.
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).
This code has been tested on Red Hat Enterprise Linux Server 7.9 (64 bit) with a Intel Xeon(R) CPU E5-2680 v4@ 2.4GHz x 56 and a Tesla P100 (2X) GPU graphics card.
For software specific dependencies, please check out the requirement.txt file.
No specialized hardware is required to run this code.
Installation and running the scripts typically takes few minutes.