{"id":34046,"date":"2020-12-02T18:00:02","date_gmt":"2020-12-02T17:00:02","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=34046"},"modified":"2024-03-22T11:20:12","modified_gmt":"2024-03-22T10:20:12","slug":"chan-zuckerberg-initiative-recognises-embl-scientists","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/lab-matters\/chan-zuckerberg-initiative-recognises-embl-scientists\/","title":{"rendered":"Chan Zuckerberg Initiative recognises EMBL scientists"},"content":{"rendered":"\n

Christian Tischer leaves behind the stark white walls of his home office to bask in a sensory contrast of autumnal colours and the musty scent of decaying leaves. Even while he tries to break away so he can return to his work with fresh perspective, the daily puzzles continue to occupy his mind. Nevertheless, it\u2019s just the right retreat to help centre his thoughts, and has become a routine part of his scientific process.<\/p>\n\n\n\n

A physicist who has spent a total of 15 years at EMBL, Christian is one of four EMBL scientists recognised this week by the Chan Zuckerberg Initiative (CZI) for their expertise as technology developers in the life sciences. \u201cCZI realised that an effective way to help science is to enable technology,\u201d he says.<\/p>\n\n\n\n

All of these EMBL recipients are bold, unconventional problem solvers. Claire Deo, Anna Kreshuk, Robert Prevedel, and Christian Tischer look for novel, elegant solutions that don\u2019t just address one specific problem. And though none of them is a biologist, they use technology to raise the bar for biological research. It\u2019s also clear that a pandemic may have changed the way they work, but not their drive.<\/p>\n\n\n\n

\u201cOur goal is to support the advancement of imaging technologies and provide access to and training on these state-of-the-art tools so that researchers can drive towards discoveries,\u201d says CZI Imaging Program Officer Stephani Otte. \u201cBy collaborating closely with the imaging community and providing both funding and expertise in technology development, we hope to help make the next breakthroughs in imaging possible.\u201d<\/p>\n\n\n\n

Transforming images into something measurable<\/strong><\/h2>\n\n\n\n

Heading EMBL\u2019s Centre for Bioimage Analysis<\/a> (CBA), Christian\u2019s job is to support scientists in turning their microscopy data into something that can be measured, enabling them to draw quantitative and biophysically meaningful conclusions from images.<\/p>\n\n\n\n

\"Researcher
Christian Tischer\u2019s CZI award is an Imaging Scientists grant that will fund his position for three years. Credit: Aleksandra Novakovic<\/figcaption><\/figure>\n\n\n\n

Christian\u2019s CZI award is an Imaging Scientists grant that will fund his position for the next three years, with the possibility of an extension for a further two years. He is one of only 39 scientists worldwide to receive this honour in 2019.<\/p>\n\n\n\n

At EMBL, he has worked as a Staff Scientist in the Advanced Light Microscopy Facility<\/a> (ALMF) for the past 10 years, and for three years has also headed the CBA. This followed postdoctoral work at the AMOLF institute in Amsterdam and a PhD at EMBL, where he studied intracellular signalling mechanisms and cytoskeleton dynamics using advanced microscopy techniques.<\/p>\n\n\n\n

\u201cBioimage analysis is concerned with the automated quantification of microscopy images and is a relatively recent profession,\u201d Christian says. \u201cDecades ago, scientists would take pictures of interesting cells and publish one picture. Today, people like me help them convert multiple images into quantitative information. At the beginning, we have images from an organism; in the end, we have numbers.\u201d<\/p>\n\n\n\n

Biologists producing data consistently outnumber the analysts developing novel algorithms and providing services in bioimage analysis. This is why CZI sees supporting these analysts as an important need for advancing science.<\/p>\n\n\n\n

\u201cThis is where we bottleneck,\u201d Christian says. \u201cBiologists come in with their data, but very often it\u2019s not just about straightforward image analysis. You have to really discuss with them the biological question they want to answer. I\u2019ve had to learn a lot about biology. What makes this job both interesting and challenging is that it\u2019s extremely interdisciplinary.\u201d<\/p>\n\n\n\n

Using light and sound to see deeper into biological tissue<\/strong><\/h2>\n\n\n\n

Claire Deo<\/a> has a rainbow of molecular probes that will play a vital role in developing a hybrid microscope that harnesses light, sound, and adaptive optics to take non-invasive microscope imagery to a deeper level than ever before.<\/p>\n\n\n\n

That\u2019s the goal for this second CZI award, in \u2018Deep Tissue Imaging\u2019, which recognises EMBL group leaders Claire Deo and Robert Prevedel<\/a>. The two EMBL scientists \u2013 one a chemist, the other a physicist and microscopy expert \u2013 will combine their talents with Sylvain Gigan, a colleague at the Kastler Brossel Laboratory at the \u00c9cole normale sup\u00e9rieure in Paris, known for his work in adaptive optics.<\/p>\n\n\n\n

\"Female
Claire Deo is one of two EMBL scientists to be recognised with CZI funding to advance deep tissue imaging. Credit: Massimo Del Prete\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cMy lab exploits photoacoustics, a technique that creates images using light and sound,\u201d Robert explains. \u201cClaire develops sensors or probes with molecules that can light up in either the sound or light modality, and Sylvain is an expert in a field known as \u2018extreme\u2019 adaptive optics.\u201d<\/p>\n\n\n\n

Adaptive optics is best known in astronomy, where it\u2019s used to adjust for atmospheric distortion in telescope images. In microscopy, it can be used to adjust for the scattering of light or other signals, which is an unavoidable part of looking deeper into tissue. Light can\u2019t penetrate biological tissue without quickly becoming diffuse, while the longer wavelength of ultrasound allows it to penetrate further, but makes it less able to resolve small details.<\/p>\n\n\n\n

\"Male
Robert Prevedel will work together with Claire Deo to develop a hybrid microscope that harnesses light, sound, and adaptive optics to take non-invasive microscope imagery to a deeper level than ever before. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

Adaptive optics will help to resolve these problems by seizing on the strengths of the different imaging modalities, enabling the team to extend the high-resolution field of view deeper into biological tissue. The million-dollar CZI award supports their efforts over the next two-and-a-half years.<\/p>\n\n\n\n

Claire\u2019s postdoctoral research at the Howard Hughes Medical Institute\u2019s Janelia Research campus near Washington, DC, took her chemistry background to a new level. The researchers there were predominantly imaging cells, and Claire quickly found her niche as a developer of chemical tools in this field of microscopy. At EMBL, she uses this expertise in creating new molecular tools to advance imaging technology. \u201cI\u2019m currently developing molecules that turn on and off in response to light, to produce fluorescence or a photoacoustic signal,\u201d she explains. \u201cWhat really drives me is finding ways to make and apply new molecular tools to enable new scientific discoveries.\u201d<\/p>\n\n\n\n

Robert started his transition from physics to biophysics as a postdoc in Vienna, where he looked at ways to develop high-speed imaging techniques to record from neuronal circuits. He\u2019s excited about potential neuroscience applications for the technologies he and Claire are developing. \u201cAt the moment, we can probe to depths of around 0.5 mm inside a mouse brain and observe its neuronal activity,\u201d he says. \u201cBut we want to go deeper, to study other important brain regions such as the hippocampus, which plays an important role in memory formation and learning.\u201d<\/p>\n\n\n\n

Automating science so researchers can do more<\/strong><\/h2>\n\n\n\n

Anna Kreshuk<\/a> builds and fine-tunes computational methods to solve scientists\u2019 research problems \u2013 sometimes before they were aware such a solution could<\/em> exist.<\/p>\n\n\n\n

Anna\u2019s CZI award provides year-long funding under the heading of \u2018Essential Open Source Software for Science\u2019. It will enable her to take her easy-to-use machine learning software, ilastik<\/a>, and build bridges from it to other open source tools, resulting in an improved user interface and faster execution. \u201cIt\u2019s extremely difficult to find funding for the essential but mundane tasks that make software so much better on the inside, but are not necessarily obvious to end users,\u201d explains Anna. \u201cCZI provides that kind of funding, allowing us to develop better software that is more maintainable, more future proof, and more open to contributions from the community. It\u2019s what every open source software development team dreams of!\u201d<\/p>\n\n\n\n

\"Female
Anna Kreshuk\u2019s CZI award provides year-long funding under the heading of \u2018Essential Open Source Software for Science\u2019. Credit: Marietta Schupp\/EMBL<\/figcaption><\/figure>\n\n\n\n

ilastik is a popular open source tool that brings machine learning-based image analysis to users without requiring them to have computational expertise. Anna got involved in the development of ilastik while a postdoc in the group of Fred Hamprecht, a Professor for Image Analysis and Learning at Heidelberg University. She brought ilastik to EMBL when she became a group leader here in 2018. The ilastik toolkit<\/a> is a system that anyone can use to leverage machine learning algorithms that easily segment, classify, track, and count cells or analyse other experimental data. \u201cI hope that with ilastik we will gradually move more and more image analysis tasks to the \u2018easy\u2019 category and allow people to plan their experiments as if that bottleneck didn\u2019t exist,\u201d Anna says.<\/p>\n\n\n\n

While microscopy remains the primary application driving its development, ilastik has been used in a variety of other areas, including analysis of satellite images. Anna\u2019s plan is to provide ilastik with an improved front end using a fast, interactive, multi-dimensional open source image viewer called napari. She will also use an open source task distribution system to speed up the software. This will reduce costs and provide an improved user experience, bringing advanced image analysis methods to a diverse range of scientists.<\/p>\n\n\n\n

\u201cFor any scientist, there is an obvious thrill in thinking of something no one has thought of before, the thrill of being proven right through your experiments,\u201d Anna says. \u201cAnd for us, on top of all that, there is the joy of going beyond an intellectual exercise and seeing our work used by others for their own research.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

The Chan Zuckerberg Initiative has recognised four EMBL researchers with their most recent awards, showing how tech trailblazers are integral to advancing science and medicine.<\/p>\n","protected":false},"author":100,"featured_media":34082,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[17597,3],"tags":[5620,5104,149,5618,506,54,227,505,1020,43,598,602,604,79,3622,5616,3720,464,3618,1770],"embl_taxonomy":[3972,18837,18863,19313,19093],"class_list":["post-34046","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-embl-announcements","category-lab-matters","tag-adaptive-optics","tag-almf","tag-award","tag-bioimage-analysis","tag-chan-zuckerberg","tag-chemical-biology","tag-core-facility","tag-czi","tag-deo","tag-heidelberg","tag-imaging","tag-kreshuk","tag-machine-learning","tag-microscopy","tag-open-source","tag-photoacoustics","tag-physics","tag-prevedel","tag-software","tag-technology","embl_taxonomy-advanced-light-microscopy-facility","embl_taxonomy-anna-kreshuk","embl_taxonomy-claire-deo","embl_taxonomy-kreshuk-group","embl_taxonomy-robert-prevedel"],"acf":{"embl_taxonomy_term_who":false,"embl_taxonomy_term_what":false,"embl_taxonomy_term_where":false,"featured":true,"show_featured_image":false,"color":"#007B53","link_color":"#fff","article_intro":"

EMBL tech trailblazers awarded for multidisciplinary collaborative projects that drive forward research<\/p>\n","related_links":[{"link_description":"EMBL Advanced Light Microscopy Facility","link_url":"https:\/\/www.embl.de\/services\/core_facilities\/almf"},{"link_description":"Research in the Deo group","link_url":"https:\/\/www.embl.de\/research\/units\/cbb\/deo"},{"link_description":"Research in the Prevedel group","link_url":"https:\/\/www.embl.de\/research\/units\/cbb\/prevedel"},{"link_description":"Research in the Kreshuk group","link_url":"https:\/\/www.embl.de\/research\/units\/cbb\/kreshuk"},{"link_description":"Chan Zuckerberg grant for Global 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