Home
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., preprint link
The raw input data is available via link.
NB: First, make sure that the required software and plugins are installed.
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).
The whole workflow is split into three parts:
- Averaging of basal bodies per cell
- Normalization (rescaling) of averages among cell
- Quantification of proteins localizations
