Squid: Simplifying Quantitative Imaging Platform Development and Deployment

Abstract

With rapid developments in microscopy methods, highly versatile, robust and affordable implementations are needed to enable rapid and wide adoption by the biological sciences community. Here we report Squid, a quantitative imaging platform with a full suite of hardware and software components and configurations for deploying facility-grade widefield microscopes with advanced features like flat field fluorescence excitation, patterned illumination and tracking microscopy, at a fraction of the cost of commercial solutions. The open and modular nature (both in hardware and in software) lowers the barrier for deployment, and importantly, simplifies development, making the system highly configurable and experiments that can run on the system easily programmable. Developed with the goal of helping translate the rapid advances in the field of microscopy and microscopy-enabled methods, including those powered by deep learning, we envision Squid will simplify roll-out of microscopy-based applications - including at point of care and in low resource settings, make adoption of new or otherwise advanced techniques easier, and significantly increase the available microscope-hours to labs.

multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection

“…Pysero also enables visualization and interpretation of antibody responses. The data we report were acquired on Scienion plate reader and Nautilus, a plate reader designed with low-cost components to increase accessibility to this technology (34). Thus, this platform is usable by a large range of research and public health studies.…”

Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox

“…Despite the many advantages of smFRET, it is not widely used outside of specialist labs due to the high costs of commercial instruments and a lack of simple, self-build alternatives. A growing trend towards development of low-cost opensource microscopy is taking place and other platforms have recently emerged, including Planktonscope 17 , OpenFlexure Microscope 18 , Flexiscope 19 , miCube 20 , liteTIRF 21 , and Squid 22 . Herein the study describes the protocol for using the smfBox, a recently developed cost-effective confocal set-up capable of measuring the FRET efficiency between two dyes on freely diffusing single molecules.…”

An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

“…9 The application of machine learning algorithms in microscopy image analysis potentially helps to find correlations in data with previously trained networks 10,11 or in a completely unsupervised manner. 12 Notable are projects aimed at segmenting cells in micrographs tracking morphological changes, 13 improving the signal-to-noise ratio to enable low-photon dose imaging 14, 15 16,17 or even performing augmented microscopy tasks.…”

“…In terms of the modern bio-lab, many research groups have already shown that different do-it-yourself (DIY) hardware can also be applied to biological questions and that it is even possible to build customized solutions using 3D printing and electronic setups, which significantly simplify the laboratory process. 13,[20][21][22][23][24][25] Nevertheless, it is worth noting that the inhibition threshold for replication is still too high. After all, it requires a broad knowledge of electronics, 3D design and printing, programming and the subsequent frustration-dominated assembly of the devices.…”

“…Even if open hardware is easily accessible, there is often a lack of high-quality documentation to finally replicate the result. On the other hand, projects such as the 3D printed OpenFlexure Microscope 23 , the Octopi/SQUID project 13 and the cellSTORM microscope 22 come with a fully illustrated manual that enables highperformance microscopy on a stand-alone or modular scale, as well as turning a smartphone into a Single Molecule Localization Microscopy (SMLM) setup. These projects have all been replicated by the growing community of microscopy users.…”