Full-Stack Microscopy Handbook

Biology experiment and biomedical R&D requires understanding of science, hardware, and engineering. Full-stack microscopy provides practical review of design & implementation across whole structure of projects: from envisioning experimental setups to programming control and data analysis

This handbook is designed to be a general reference to a wide range of topics, potentially missing a lot of details. Where possible, we provide specific references where you can learn more; in other cases we would recommend asking for assistance more knowledgeable colleagues both online and offline.

Contributions are welcome! Submit an issue or fork the repository on GitHub, make changes, and submit pull request

Built with the Jupyter Book and Github Pages.

Assembled by Andrey Andreev

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?
• Implementation with Arduino
• DAQ (NI DAQs)
• Function/Waveform generators
• Sensors: temperature, humidity, flow, light
• 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