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This repository contains a set of Fiji macros
for extraction, averaging and normalization (rescaling) of basal bodies (BB)
from expansion microscopy volumetric datasets.
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.
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.
Prior to analysis a deconvolution was performed.
The whole workflow is split into three parts:
- Averaging of basal bodies per cell;
- Normalization (rescaling) of averages among cell;
- Quantification of proteins localizations.
Please, read about organization of files and folders structure of the workflow, it is important.
Developed in Cell Biology group of Utrecht University.
The plugin and this wiki are under constant development.
E-mail for any questions, feedback, errors or suggestion
or tag @ekatrukha at image.sc forum.