Adaptive optics for microscopy

Practical guides to implementation

A repository for beginners guides, hints, tips and tricks on how to implement adaptive optics in microscopes and related optical systems. Hosted by the Dynamic Optics and Photonics Group, Department of Engineering Science, University of Oxford.

Adaptive Optics is a valuable tool that can enhance the performance of a broad range of optical systems, but it is often considered challenging to implement. This website provides a range of information to help understand and implement this technology, particularly for microscopy and related methods.

To learn more about the motivation for the site, see the About page. The documents themselves can be found in the Documents section below. If you don’t know where to start, the Basic introduction document gives a broad introduction to the field. Finally, to give feedback or ask any questions, please use the Contact form.

This document provides an introduction to adaptive optics for microscopy from a practical perspective.
This tutorial explains the specifics of how to set up and align the depletion beam of a STED microscope that includes a spatial light modulator (SLM).
We present two protocols for the alignment of the pinhole in a confocal microscope. The first utilizes motorized scans in the X-Z plane; while the second addresses the condition with only manual axial translation. Both protocols are relevant for reflection and fluorescence mode confocal microscopes.
This document presents details of using an SLM in a general AO experiment.
This document describes the use of a deformable mirror in closed-loop using a Shack-Hartmann sensor.
This document describes practical guidelines for the design and implementation of AO systems for microscopes.
Here we present BeamDelta, a simple tool to help align optical systems.
This tutorial discusses the static calibration of a deformable mirror using a Twyman--Green interferometer setup, combined with single-frame fringe analysis for phase extraction. We provide a reference implementation for this method in the form of a toolbox written in Python. In addition, we include detailed instructions to build a compact, slot-in interferometer. This protocol, accompanying software, and hardware design facilitate calibration of deformable mirrors for a range of applications.
This tutorial provides a protocol along with Python code to update the wavefront corrector control matrix and command vector while performing Shack-Hartmann sensing with an arbitrarily shaped pupil for both zonal and modal control methods.
This experimental protocol describes several procedures related to the operation of an imaging system based on wavefront control and step-index multimode optical fibres (MMFs). It is assumed that such an imaging system is already built and aligned, without an MMF. This protocol aims at providing guidance to new users of the system.
This user manual explains how to install and use the svmPSF plugins for Fiji/ImageJ. The svmPSF plugin models a spatially variant PSF into a series of spatially invariant PSFs for image deconvolution.
This tutorial describes the principles and practical implementation of sensorless adaptive optics.
This note explains the context and derivations of normalised coordinates and “rules of thumb" frequently used in the estimation of resolution of microscopes.