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Full-Stack Microscopy Handbook

Basics of a custom microscope

What makes a microscope?
Optical design
Light sources
Detecting light
Hardware design for microscopy
Alignment and debugging the microscope
How to find more help

Fluorescence

Why we care about fluorescence phenomena
Large and small fluorescent molecules
Fluorescent proteins
Spectra and filters
Special cases of fluorescence

Designing experiments

Designing microscopy experiments
Sample experiments
Super-resolution microscopy experiments

Controlling and synchronizing devices

Making devices talk to each other
Serial port: ASCII commands
How can we generate signals?
Devices can’t follow signals perfectly
Example code to generate signals
Connecting devices to Micro-Manager 2.0

Data management and analysis

Types of microscopy data
Data storage problem
Presentation of microscopy data
Analysis of microscopy data

Repository
Open issue

.md

Types of microscopy data

Contents

Two-dimensional datasets
Extracting image metrics
Temporal data

Types of microscopy data#

Two-dimensional datasets#

Extracting image metrics#

Temporal data#

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Connecting devices to Micro-Manager 2.0

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Data storage problem

Contents

Two-dimensional datasets
Extracting image metrics
Temporal data

By Andrey Andreev

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