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Getting Started
About this Manual
Introduction to Fiji
Basic Navigation in Fiji
Working with and Visualising Images
Adjusting Brightness and Contrast
Colour and Intensity Data Visualisation
Calibrating and Adding a Scale Bar
Fluorescent Images
Opening Proprietary Data Sets
Visualising 3D and Live Data
Analysing Images
Area and Intensity of Stain
Cell Counting in 2D and 3D
Cell Segmentation and Analysis
Cell Morphology and Shape Change
Intensity Over Time
Image Filters - Fixed and Live Data
Distance Measurment
Measuring Branching Structures in 2D and 3D
Useful Tools
Stiching Images
Image Stack Alignment
Advanced Thresholding - Machine Learning
Coding Macros
About the Coding Modules
Basic Macro Recording
An Introduction to Variables
Batch Processing
Custom Data Loging
Looping for ROIs
Custom Dialog Boxes
Arrays
Functions
About the Coding Modules
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