Home - UU-cellbiology/averageBasalBodies GitHub Wiki

Welcome to the averageBasalBodies wiki!

This repository contains a set of Fiji macros
for extraction, averaging, normalization (rescaling), and quantification
of basal bodies (BB) from expansion microscopy volumetric datasets.

This workflow corresponds to the manuscript:
"Microtubule organization and molecular architecture of ciliary basal bodies in multiciliated airway cells"
van Grinsven et al., Current Biology, 2026 PubMed link.
The version used in the manuscript is 0.0.2
The paper's raw input data is available via link.

Higher version numbers contain bug fixes and optimizations.
Please use the most recent one for your analysis.

NB: First, make sure that the required software and plugins are installed.

Input data

The input data represents multi-channel volumetric images of apical part of respiratory epithelia cells.
They are stained for the "total protein" and proteins of interest and expanded using ExM.
The pan-ExM channel ("total protein" NHS staining) is used as a reference registration channel.
It is assumed that all data has the same voxel size.
For our data, prior to analysis, a deconvolution was performed (but it is optional).

Workflow

The whole workflow is split into three parts: