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Welcome to the extractBasalBodies wiki!

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

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This workflow corresponds to the published manuscript:
Name of the manuscript and link

The raw input data is available here (link to data).

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 parts

The whole workflow is split into three parts:

1. Averaging of basal bodies per cell
2. Normalization (rescaling) of averages among cell
3. Quantification of proteins localizations