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Department of Chemical Engineering and Biotechnology

OptiJ image showing 3D structure of a mouse lung

Researchers from our Laser Analytics group have developed a low-cost, open-source imaging system that can visualise groups of cells or organ tissues without cutting the tissues.

Optical projection tomography (OPT) is an imaging technique similar to that found in airport security scanners and used in medical CT (computed tomography) scans. CT scans work by passing x-rays through a 3D object while it is rotating, and using the resulting pattern to recover its 3D shape.

OPT uses visible light instead of x-rays, and is typically used to examine samples which are millimetres in scale.

“The method can be thought of as an inverse problem in which you try to recover the shape of an object by taking pictures of its shadow,” says PhD student Pedro Vallejo Ramirez. “In OPT, we illuminate a translucent object with an LED and take pictures of the object as it rotates, and reconstruct a 3D rendering of the object using an algorithm called filtered back-projection. OPT has previously been used to examine the 3D morphology of zebrafish, mouse embryos, plants, and fruit flies, among others.”

The technique is useful for imaging large samples (in this context, tens of millimetres) that are difficult or impossible to examine using traditional microscopy methods. Unlike in traditional microscopy techniques, OPT can’t resolve fine features or structure needed when examining single cells, but it can visualise groups of cells or whole organs.

While there have been major improvements in the resolution and acquisition time of OPT, most of its applications require advanced technical expertise, expensive equipment and bespoke software for reconstructions. The collaborative work of Vallejo Ramirez, supervisor Professor Clemens Kaminski, and scores of other researchers in our department is looking to change that with their open-source solution: OptiJ.

Originally conceived as a team challenge for the 2015 student intake of our Centre for Doctoral Training in Sensor Technologies for a Healthy and Sustainable Future, the OptiJ project aims to enable more general uptake of the OPT technique in the microscopy community by offering a low-cost, open-source system.

“The 2015 Sensor CDT cohort built a working prototype of the open-source device and software that could image large samples during the summer of 2016,” says Vallejo Ramirez. “I jumped on the project when I started my PhD in October 2016 and worked on characterising the system, as well as following through a collaboration with AstraZeneca to image a set of excised mouse lungs.

“We present a low-cost, open-source hardware and software system with detailed instructions on how to build and operate the system that any lab can readily adopt.

“One of the main differentiators of our publication was the 3D visualisation of large organ samples without cutting the tissue. Our system is capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution.”

OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction.

“I am genuinely excited about this effort, which represents an output that originates from one of the so-called Sensor Team Challenges in which students from the Sensor CDT work together to address a difficult research problem over a short period of time,” said Professor Clemens Kaminski. “The work presented here went well beyond the 15 weeks originally allocated for the team challenge and seeded valuable follow on work that was led by Pedro. The paper is the culmination of this effort.

“Using open technologies in clever new ways permits us to address state of the art imaging challenges in the biomedical field. What the students have achieved here is tremendous taking an idea  all the way from prototype to application.  It enables high quality imaging in a cost effective and better way than existing technologies can achieve, opening up tomographic optical imaging to laboratories across the world.”

The system can be used to study observable properties of diseases in mouse organs to understand the effect of certain diseases in groups of cells within the context of the whole organ. It could also help to visualise the effectiveness of drugs or therapeutics in targeting these diseased cell groups inside the organs.

“OptiJ contributes to a growing number of open-source systems for biological imaging that hope to make instrumentation more widely accessible to scientists who might not have the budget to purchase commercial instruments,” says Vallejo Ramirez.

“We hope the open-source plugins and hardware developments in OptiJ will be adopted and used by the microscopy community for other applications of imaging large samples.

“After OptiJ I’ve worked to develop hardware and software tools for quantitative bio imaging in disease models for Parkinson's and HIV, and I am continuously looking for exciting new biological problems to tackle with optics.”

Read the full paper, published in Nature Scientific Reports.

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