Home

Welcome to the extractBasalBodies wiki!

This repository contains a set of Fiji macros/GNU Octave scripts
for basal bodies extraction from expansion microscopy images.

---

Here is the description of the workflow.

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

The initial data represents multi-channel volumetric images of basal bodies with ExM.
The whole workflow is organized as a sequence of steps.

Please, read about organization of files and folders structure of the workflow, it is important.

One channel is used as a reference alignment channel.
Usually, it is pan-ExM channel (whole protein NHS staining).

Workflow description

• Step 0: auto ROIs generation
• Step 1: detecting basal bodies (BB) in 3D
• Step 2: extracting basal bodies