Tools and Protocols

Fluorescence   Leica resources  High Content Imaging/ Analysis

General Microscopy


Molecular Expressions (FSU),  Microscopy Resources Center (Olympus),  Education in Microscopy and Digital Imaging (Zeiss) and MicroscopyU (Nikon). Four quite exhaustive sites (very similar in content and organization), covering everything from basic microscopy to more specialized subjects.

ScienceLab (Leica), less organized but searchable collection of articles, webinars and tutorials on a variety of subjects.

BitesizeBio, Microscopy and Imaging, short articles and company-sponsored webinars covering a variety of different microscopy-related subjects.

iBiology Microscopy Course, lecture videos from basic microscopy to specialised applications.

Some introductory reviews:

Fluorescence microscopy (Nature Methods)

Optical sectioning microscopy (Nature Methods)

Deep tissue two-photon microscopy (Nature Methods), A simple introduction to multiphoton microscopy (Journal of Microscopy)

Second harmonic imaging microscopy...(Nature Biotechnology)

Fluorescence lifetime imaging-techniques and applications (Journal of Microscopy)

Image quality:

Seeing is believing? A beginners' guide to practical pitfalls in image acquisition (Journal of Cell Biology)

Accuracy and precision in quantitative fluorescence microscopy (Journal of Cell Biology)

Fluorescence tools

Interactive databases of fluorophore excitation/ emission curves and filters:

Spectraviewer (Life technologies), covers mainly their offering of fluorophores, allows to customize the filter specifications.
Curvomatic (Chroma) and Searchlight (Semrock), both are filter manufacturers and only list their filter-sets. Their databases contain many fluorphores that are not listed in the Spectraviewer.   

Handbook on filters for fluorescence microscopy (Chroma), a compilation of filter design and terminology.

2-photon excitation:

2-photon excitation spectra (drbio.cornell)
Two-photon absorption properties of fluorescent proteins (Nature methods)

Fluorescent dyes and techniques:

Molecular Probes School of Fluorescence (ThermoFisherScientific)
Fluorescent dyes overview (Leica)
Molecular Probes Handbook (ThermoFisherScientific)
Fluorescent Probes (BOC Sciences)

Fluorescence and IHC reference images:

Human Protein Atlas
The Cell Image Library

antibody resource
BenchSci (recommended)
biocompare antibodies

Leica resources

Information about Leica microscopes

Leica home page

Leica objectives, explains the objective nomenclature and objective specifications.

PDF iconFiltercubes

ScienceLab, searchable Leica microscopy resources site with articles, webinars, tutorials.

Leica AF Lite, free download, allows to view .lif images and save them in open image formats.

PDF iconPMT and HyD detectors, explains how Hybrid detectors offer higher sensitivity than standard PMT detectors. 

High Content Imaging/ Analysis

Operetta Application Notes (PerkinElmer), High Content Screening page with examples for cellular assays and analysis methods.

High Content Screening Assay Development Guidelines, introduction to High Content Imaging/ Screening and best practices for assay development.

Tips for HCS-assays (Enzo)
Tips for cell-based assays (Enzo)

Assay quality: the Z’-Factor (Journal of Biomolecular Screening), commonly used simple statistical method to evaluate HTS/ HCS assays.

Bioanalysis    Microarray   qPCR   Pyrosequencing   GeneSpring   Agilent Genomics Workbench        



PDF iconBioanalyzer Reagents Selection Guide

Agilent 2100 Expert Software-users Guide

Agilent 2100 Bioanalyzer Support Tool Box download



PDF icon One-color Gene expression microarray workflow

MIAME -Minimum information about a microarray experiment (Nature)

Agilent Gene Expression protocols download

Feature Extraction  Software 11.5- Reference Guide




qPCR software analysis Auto-qPCR (Neuro)

Real Time PCR Handbook (Life Technologies)

Guide to performing Relative quantitation of gene expression (Applied Biosystems)

Applied Biosystems ®ViiA ™7 Real-Time PCR System - Getting Started Guide

The MIQE Guidelines-Minimum Information for Publication of Quantitative Real-Time PCR Experiments

Pitfalls of Quantitative Real-Time Reverse-Transcription PCR (Journal of biomolecular techniques)

Pitfalls and recommendations for microRNA expression analysis using qPCR (Exiqon)




PDF iconPyrosequencing workflow

PDF icon PyroMark Q24 and Q96-MD Reagents and Consumables

DNA Methylation Analysis Protocol (Nature Protocols)

Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis (Biotechniques)

PCR optimization for pyrosequencing (Biotage)

Guidelines for allele quantification (Standford University)

Pyrosequencing troubleshooting guidelines (Standford University)


GeneSpring software

GeneSpring  Support: Video Tutorials, Webinars, Demo Datasets

Agilent earray: Catalog and Custom Microarray designs

PDF iconTen pitfalls of microarray analysis-Agilent technical notes

GeneSpring manual (Agilent)


Agilent Genomics workbench software

CGH interactive analysis (Agilent)

Methylation analysis (Agilent)

ChIP interactive analysis (Agilent)

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