OpenSpinMicroscopy: an open-source integrated microscopy platform

  title={OpenSpinMicroscopy: an open-source integrated microscopy platform},
  author={Emilio J. Gualda and Tiago Vale and Pedro Almada and Jos{\'e} A. Feij{\'o} and Gabriel G. Martins and Nuno Moreno},
  journal={Nature Methods},
acKnoWLedGments We thank V. Surendranath for help with photography, H. Bellen (Baylor College of Medicine, Texas) for the Csp-sGFP transgene, and S. Singh, Sonal and S. Simmert for seeding the wiki with material during the Dresden International PhD Program course. We thank B. Cox and G. Petry of the Morgridge Institute for Research for assistance with 3D printing and parts fabrication. J.S., L.S. and K.W.E. were supported by US National Institutes of Health grants RC2GM092519 and R01CA136590. S… 

506 CHAPTER 27 Open-source solutions for SPIMage processing

A set of practical recipes that walk biologists through the complex processes of SPIM data registration, fusion, deconvolution, and time-lapse registration using publicly available open-source tools are provided.

OpenSegSPIM: a user-friendly segmentation tool for SPIM data

UNLABELLED OpenSegSPIM is an open access and user friendly 3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data. The software is designed to extract, in a

Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development

The OpenSPIM is described, which provides high resolution 3d images and time lapse recordings, and the use of two colour lasers and the benefits of two color dual-sided imaging, and is used to study the development of the embryo of the polyclad flatworm M. crozieri.

Light sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development

It is concluded that home-built microscopes, such as an OpenSPIM, together with the available open source software,such as MicroManager and Fiji, make SPIM accessible to anyone interested in having continuous access to their own light-sheet microscope.

μSPIM: A Software Platform for Selective Plane Illumination Microscopy

A control toolset, μSPIM, built around the open-source MicroManager platform that has already been widely adopted for the control of microscopy hardware is presented, making it relatively independent of the optical design of the microscope, or the hardware used to build it.

The light-sheet microscopy revolution

This paper reviews the rapid advances that have been made in one form of optical biological imaging in the last decade, namely that of light sheet microscopy. Although the concept was originally

Dual-view plane illumination microscopy for rapid and spatially isotropic imaging

The construction and use of a compact dual-view inverted selective plane illumination microscope for time-lapse volumetric imaging of living samples at subcellular resolution is described and successful implementation of the protocol results in isotropic resolution and acquisition speeds up to several volumes per s on these samples.

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

This article describes a complete experimental protocol starting with the mounting of zebrafish embryos for LSFM and explains a pipeline for subsequent registration and fusion of multiview datasets using an open source solution implemented as a Fiji plugin.

A guide to light-sheet fluorescence microscopy for multiscale imaging

This work elucidate the key developments and define a simple set of underlying principles governing LSFM, which aim to clarify the decisions to be made for those who wish to develop and use bespoke light-sheet systems and to assist in identifying the best approaches to apply this powerful technique to myriad biological questions.



Computer Control of Microscopes Using µManager

This unit provides step‐by‐step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software.

Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies

This work has developed a microscopy technique that uses optical projection tomography (OPT) to produce high-resolution 3D images of both fluorescent and nonfluorescent biological specimens with a thickness of up to 15 millimeters.

Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy

This method discriminates the specimen-related scattered background from signal fluorescence, thereby removing out-of-focus light and optimizing the contrast of in-focus structures, and provides rapid control of the illumination pattern, exceptional imaging quality and high imaging speeds.

Selective plane illumination microscopy techniques in developmental biology

This review compares the benefits and challenges of light-sheet microscopy with established fluorescence microscopy techniques such as confocal microscopy and discusses the different implementations and applications of this easily adaptable technology.

Software for bead-based registration of selective plane illumination microscopy data

It is shown here how bead-based and intensity-based multi-view reconstruction on 7-view acquisition of Drosophila embryo expressing His-YFP affects the registration error of the SPIM registration plugin.

Imaging life with thin sheets of light

The revival of light-sheet microscopy opens new possibilities for the imaging of living processes and its applications in medicine, science and engineering.