Biology subjects

Babcock, H.

Publications and source records attributed to Babcock, H..

3 recordsLinked to original sources

bioRxiv2018

Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software

With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. We generated realistic simulated datasets for popular imaging modalities - 2D, astigmatic 3D, biplane 3D, and double helix 3D - and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.

biophysics↗

bioRxiv2017

Multiplane and Spectrally-Resolved Single Molecule Localization Microscopy with Industrial Grade CMOS Cameras

In this work we explore the use of industrial grade CMOS cameras for single molecule localization microscopy (SMLM). We show that the performance of these cameras in single imaging plane SMLM applications is comparable to much more expensive scientific CMOS (sCMOS) cameras. We show that these cameras can be used in more demanding biplane, multiplane and spectrally resolved SMLM applications. The 10-40x reduction in camera cost makes it practical to build SMLM setups with 4 or more cameras. In addition we provide open-source software for simultaneously controlling multiple CMOS cameras and for the reduction of the movies that are acquired to super-resolution images.

biophysics↗

bioRxiv2016

Analyzing Single Molecule Localization MicroscopyData Using Cubic Splines

The resolution of super-resolution microscopy based on single molecule localization is in part determined by the accuracy of the localization algorithm. In most published approaches to date this localization is done by fitting an analytical function that approximates the point spread function (PSF) of the microscope. However, particularly for localization in 3D, analytical functions such as a Gaussian, which are computationally inexpensive, may not accurately capture the PSF shape leading to reduced fitting accuracy. On the other hand, analytical functions that can accurately capture the PSF shape, such as those based on pupil functions, can be computationally expensive. Here we investigate the use of cubic splines as an alternative fitting approach. We demonstrate that cubic splines can capture the shape of any PSF with high accuracy and that they can be used for fitting the PSF with only a 2-3x increase in computation time as compared to Gaussian fitting. We provide an open-source software package that measures the PSF of any microscope and uses the measured PSF to perform 3D single molecule localization microscopy analysis with reasonable accuracy and speed.

biophysics↗