Virtual Pub Special Edition


October 12, 2022
Virtual Pub

Imaging technologies are becoming increasingly complex and ever more expensive, reducing the general accessibility and potential reach of cutting-edge microscopy. Open microscopy addresses this issue – and many imaging scientists are committed to making microscopy hardware and software solutions openly available to a wide audience. The Special Edition Virtual Pub “Open Hardware in Microscopy” will highlight these developments, by featuring presentations of a number of open hardware projects in light and electron microscopy. 

From open and modular hardware framework for light microscopy to adapting legacy commercial microscope frames to new modalities in order to obtain super-resolution performance, there is something for everyone at this Virtual Pub, so don’t miss out!

Full program & abstracts (see below)

Mark your calendars

The Special Edition Virtual Pub “Open Hardware in Microscopy” will take place on Friday, November 4th, from 13:00-15:00 CET. Please join us for an exciting afternoon with great speakers and lots of exciting talks! No registration is necessary. 

How to connect:

Join via internet:

https://us02web.zoom.us/j/760003029
via phone:

Meeting ID: 760 003 029

Find your local number: https://zoom.us/u/acj97wMY13

Full program:

13:00-13:10

Welcome

13:10-13.25

Johannes Hohlbein, Wageningen University and Research

Open microscopy in the life sciences: Sharing is caring

13.25-13.40

Gaby Martins, Instituto Gulbenkian de Ciência IGC

OPenT and mesoscopic open-source imaging

13.40-13.55

Paul French, Imperial College London

openFrame: an open, modular platform for microscopy and high content analysis

13.55-14.10

Hannah Heil, Instituto Gulbenkian de Ciência IGC

The field guide to 3D-printing in microscopy 

14.10-14.25

Marek Malac, University of Alberta

An introduction to NanoMi: an open source electron microscopy platform

14.25-14.40

Benedict Diederich, University Jena

From Ideas to Globally Accessible Instruments 

14.40-15.00

Discussion

Abstracts of the talks 

Johannes Hohlbein, Wageningen University and Research

Open microscopy in the life sciences: Sharing is caring

Together with other colleagues enthusiastic about open science, we recently published a comment on the past, presence and future potential of open microscopy (https://doi.org/10.1038/s41592-022-01602-3). Here, I will iterate on some of the key points with a focus on single-molecule localisation microscopy (SMLM). SMLM allows monitoring molecular interactions in live cells and other complex samples. A few years ago, we developed the miCube microscopy framework to increase the general accessibility and affordability of SMLM. We were intrigued to see how quickly other groups came up with new ideas and improvements in addition to our own developmental milestones including new algorithms for ultrafast data analysis and the addition of adaptive optics for localising proteins in turbid media. These few examples demonstrate the huge potential of open microscopy in enabling interdisciplinary science and lowering the threshold for researchers to find the best solutions for their scientific imaging challenges.

Gaby Martins, Instituto Gulbenkian de Ciência IGC

OPenT and mesoscopic open-source imaging

OPenT is an open-source project to develop a user-friendly do-it-yourself mesoscope based on optical-projection tomography (OPT). OPT allows the acquisition of projectional datasets of both bight-field (transmitted light) illumination and fluorescence, from various angles while the sample rotates in front of a camera equipped with a low magnification objective, which are subsequently transformed into stacks of 3D optical slices, using filtered back-projection reconstruction. OPenT is optimized for imaging large samples, in the few mm to few cm range. We have developed a small prototype, the acquisition software and prepared a script to pre-process the projectional datasets (a critical and demanding step in the reconstruction workflow) using the popular ImageJ toolbox. In this brief presentation I will show the basic principles of the prototype and operation, and examples of 3D datasets obtained with this prototype.

Paul French, Imperial College London

openFrame: an open, modular platform for microscopy and high content analysis

We are developing open multidimensional fluorescence imaging instrumentation, including high content analysis (HCA), super-resolved microscopy, quantitative phase imaging and optical projection tomography. For fluorescence microscopy, we are developing a modular open-source microscopy platform based on openFrame, a low-cost, modular, microscope stand that can be used for low-cost and sustainable instruments in lower resource settings or for rapid prototyping of advanced microscopy concepts. For open HCA and slide scanning, we have developed a long-range (~200 micron) optical autofocus module utilising machine learning. This can be combined with easySTORM for cost-effective single molecule localisation microscopy (SMLM) including automated multiwell plate SMLM for super-resolved HCA. We have also developed a polarization differential phase contrast microscopy (pDPC) module providing single-shot quantitative phase imaging that we are applying to label-free single cell segmentation and tracking for long time-base assays.

Hannah Heil, Instituto Gulbenkian de Ciência IGC

The field guide to 3D-printing in microscopy

The maker movement has reached the optics labs empowering researchers to actively create and modify microscope designs and imaging accessories. Especially 3D printing has had a disruptive impact on the field as it takes a completely different approach than conventional fabrication technologies, namely additive manufacturing, making prototyping in the lab available at low costs. Many examples of this trend are taking advantage of the easy accessibility of 3D printing technology. For example, cheap microscopes for education are being produced, such as the FlyPi [Chagas et al. (2017) PLOS Biology 15(7)]. Also, the highly complex robotic microscope OpenFlexure [Collins et al. (2020) Biomed. Opt. Express (11), 2447-2460 ] represents a clear desire for the democratisation of this technology. 3D printing facilitates new and powerful approaches to science and promotes collaborations between researchers, as 3D designs are easily shared. 3D printing holds the unique possibility to extend the open-access concept from knowledge to technology allowing researchers from everywhere to use and extend model structures. Here we present a review of additive manufacturing applications in microscopy, guiding the user through this new and exciting technology and giving a starting point to anyone willing to employ this powerful and versatile new tool.

Marek Malac, University of Alberta

An introduction to NanoMi: an open source electron microscopy platform

We are developing an open source electron microscopy platform that includes all components needed to assemble a working electron microscope for educational purposes and for niche applications, with a modest performance. Our goal is to contribute to the electron microscopy community by providing a publicly available design of hardware, control electronics and software for a modular, ultrahigh vacuum compatible electron microscope column. We refer to this column as NanoMi [1].

NanoMi is intended to operate below 50 keV, achieve ~10 nm spatial resolution in SEM, TEM and scanning TEM (STEM) modes, and provide electron diffraction capability. All the components, such as Einzel lens, sample stage and electronics circuitry are discrete modules that can be mounted at any location along the electron microscope column making it possible to customize the instrument.

At present, most of the individual components are tested and the hardware has been assembled into a working electron microscope column. The integration of the individual components is currently under way. The software controlling the instrument has been mostly completed. For the first implementation, we chose to utilize electrostatic Einzel lens making extensive use of work of Rempfer [2,3].

[1] nanomi.org and https://osf.io/bpj73, DOI: 10.17605/OSF.IO/BPJ73

[2] G. Rempfer, J. Appl. Phys. 57 (1985), p. 2385.

[3] Malac et. al. Micron (2022), https://doi.org/10.1016/j.micron.2022.103362

Benedict Diederich, University Jena

From Ideas to Globally Accessible Instruments

Pandemics, extinction of species and antibiotic crises: These are not dystopian scenarios of the distant future, but current, observable problem situations that people in global ecosystems are now trying to deal with and have to find a way through scientific analysis.

Science is responsible here for researching connections on a global level and, by disseminating its findings. However, a high level of technical expertise, as well as high financial investments for laboratory equipment and experiments is often required. What follows from this is a resource-related limited accessibility to the scientific tools that are necessary for researching socially relevant topics.

“Frugal Science” thinks scientific instruments from a whole new perspective. Limited by the available budget and parts, one must get creative in order to solve a scientific question posed by the society. Following this idea, we applied this method to the – in many situations – very expensive field of microscopy, in order to give a deeper insight into the microcosm for everyone, everywhere. With our modular open-source toolbox UC2 (You.See.Too.), we not only provide educational material in the field of STEM, but more so provide powerful tools that give the optical tools into the hands of those who need them the most; biologists, chemists and physicist. Acting as a rapid prototyping tool for optics, we present a new method that can capture plankton in 3D using a light-sheet and holographic setup. The “HoLiSheet” costs less than the laptop that processes the data and is fully open-source.


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