Software

Whole-brain microscopy image analysis

I’m developing tools for the analysis and visualisation of whole-brain microscopy images. This includes:

• cellfinder for 3D cell detection (paper)
• brainreg for 3D registration and atlas-based segmentation
• brainreg-segment for segmentation and analysis of bulk structures (e.g. Neuropixels probes, injection sites)

BrainGlobe

Along with Federico Claudi and Luigi Petrucco, we have developed: BrainGlobe: Open python tools for morphological analyses in systems neuroscience.

slurmio - a lightweight Python package to interface with the slurm workload manager.

See the GitHub repo here.

micrometa - parsing of whole-brain microscopy metadata.

See the GitHub repo here.

fancylog - fancier logging in Python.

See the GitHub repo here.

foci2D - measure foci per cell in 2D images

MATLAB software as used for the analysis of the proximity ligation assay in Koundouros et al. (2020). Counts the number of foci per cell in 2D, based on a segmented nuclear marker. See the GitHub repo here.

coloc3DT - measuring colocalisation of 3D functional images

Python software for measuring the colocalisation of N channels in another, segmented channel, as used in Jackman & Marcozzi et al. (2020). See the GitHub repo here.

cell-coloc3D - measure distribution of a marker per cell in a manually segmented object

MATLAB software as used for the quantification of 3D acini formation in Koundouros et al. (2020). Following manual segmentation of a structure (e.g. a spheroid), individual cells are segmented, and the expression of a marker within these cells is quantified. See the GitHub repo here.

CalciumAnalysis - analysis of calcium dynamics in 2D images.

MATLAB software as used for the quantification of calcium flux in Koundouros et al. (2020). Segments cells in 2D images and extracts the timecource of cellular calcium fluoresence. See the GitHub repo here.