LIFE SCIENCES Huron’s systems are digital microscopes


known as automated whole slide scanners. Tese systems consist of an LED light source sitting beneath a stage that holds a slide containing a tissue sample. Over this is positioned an objective lens, additional optics, and then finally an area scan CMOS RGB camera from Teledyne Dalsa. Te scanners operate by moving the stage


beneath the objective lens, while the camera captures multiple image strips of the slide, which are then combined by a computer to create a digital whole slide image. Te scanner does this for each of the 120 slides that can be loaded into the system, outputting BigTIFF images of each slide that can then be viewed on a computer and zoomed in on if detail is required on the microscopic level. A camera with a high frame rate is needed so


that the stage can be moved quickly and a whole slide imaged within a minute. ‘Te cameras we use provide 60fps at 12 megapixels. However, we run them in a windowed mode, so they’re actually running at thousands of frames per second.’ While the speed and quality of imaging in life


science is increasing thanks to the capabilities of CMOS, a resulting challenge is that a larger amount of data is now being produced that needs to be handled and processed. ‘Digital pathology, particularly concerning


whole slide scanners, is a very data-intensive application of machine vision,’ confirmed Myles. ‘We’re generating multiple gigabytes per second in the form of huge datasets.’ In general, according to Myles, the mainstream


of the life science market – particularly for the large labs processing millions of slides – therefore relies on fast scanners with powerful workstation computers attached to them. ‘We’ve been able to take some of the image


processing functions that we do – such as debayering – and perform them on a GPU inside the computer, rather than on a frame grabber,’ he explained. ‘Every scanner in our category


… has a powerful workstation with a multicore processor, a GPU and lots of hard drive space.’ Myles feels there is a big drive towards ease


of use, cost effectiveness, reliability, and ease of integration. Te systems also need to be portable, so that they can be placed on pathologists’ desks and in multiple parts of the lab, or wherever the tissue is.


Embedded automation Systems harnessing embedded imaging – where processing is moved closer to the image sensor and performed on-board the system – are already present in the life science market, and are becoming increasingly popular for automating applications in laboratory environments. ‘Laboratory automation is something that has


really picked up significantly over the past two to three years. Big companies in the medical field have taken up this trend to improve their systems with vision,’ said Martin Klahr, head of the digital imaging division at Phytec, a manufacturer of


Whole slide scanners …


are generating multiple gigabytes per second in the form of huge datasets


embedded imaging systems. ‘Increased safety and security for patients is sought aſter in the medical field now, and vision will be used to help deliver healthcare automatically around the clock.’ Phytec has many different projects in the life


science laboratory automation market, according to Klahr, not only in large hospitals, but also in smaller laboratories and even doctors’ offices. ‘Tese embedded imaging systems are becoming increasingly affordable, and could sell in the thousands per year. Tey could really increase the level of diagnosis in the field,’ he said. One such project, for which Phytec built


the image acquisition system and the control electronics, is the fully automated diagnostics system Unyvero, from molecular diagnostics firm Curetis. Te system is capable of imaging DNA markers from a patient sample and processing the results in order to make an accurate diagnosis of disease within four hours – compared to days taken by past systems. ‘Using the Unyvero system, all microbiological


processes for DNA analysis of pathogens are carried out in a fully computer-controlled laboratory cartridge,’ Klahr explained. ‘An integrated camera system captures the


Basler’s Med Ace cameras were shown attached to microscopes at the Analytica trade show


position and intensity of DNA markers in an image that is then processed on the machine –


24 Imaging and Machine Vision Europe • December 2018/January 2019


A laboratory cartridge in which DNA markers are imaged in the Unyvero analyser


using image processing electronics based on modular embedded imaging components.’ Te camera used in the system, rather


than requiring a high resolution, was instead developed to be sensitive to the particular wavelengths emitted by fluorescence of the DNA markers. Te camera head was therefore designed – on a project-specific basis with Curetis – to contain a beam splitter and an intelligent LED lighting unit, as according to Klahr the wavelength of the fluorescence is different to that of the LEDs. Te size of the camera was also important, as it had to be moved around inside the system in order to capture images of different markers in different positions within the laboratory cartridge. ‘Tis isn’t a standard USB camera,’ he


commented. ‘Te idea behind the embedded concept was that we could directly connect the CMOS sensor on our plane interface to the camera interface of the microprocessor that is used inside this embedded system.’ Te embedded system designed for the


Unyvero by Phytec contains both the camera and the complete control system that manages the multiple sensors, motors, heaters and pumps of the device, in addition to its data communication. Phytec uses a modular concept for its


embedded vision systems – it has modular microprocessor boards that can connect to its camera modules – which keeps design costs down. While Phytec currently produces all the


camera, boards and electronics of its embedded vision systems itself, for the future Klahr can see there being potential for collaboration with companies offering very sophisticated cameras for special applications, which Phytec could combine with its own embedded products. ‘For example, our current products do not


cover applications requiring a camera with very high light sensitivity,’ Klahr said, ‘so we could search for companies who have been in this market for a long time and have special products that are able to connect to embedded systems.’ O


@imveurope www.imveurope.com


Basler


Phytec and Curetis


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