Enhancing Global Access: interview with CZI grantee Federico Lecumberry

BIOIMAGE ACQUISITION AND PROCESSING CORE: BUILDING SKILLS IN BIOMEDICINE

Federico Lecumberry is a professor at the Faculty of Engineering at Universidad de la República in Uruguay. Their project, called IMAGINA, aims to develop the community’s skillset in computational bioimaging processing and analysis software, and develop original novel algorithms and software for imaging. Through their work they aim at bridging disciplines, bringing together teams of mathematicians, computer scientists and biologists, to address the needs of the field. 

What was the inspiration for your project? How did your idea for the CZI project arise?

The project IMAGINA was created before our CZI project – it was founded in 2015. I was leading my group at Institut Pasteur de Montevideo and in 2015 I started a multidisciplinary team financed by Universidad de la República with the Faculty of Medicine, called IMAGINA, with the co-PI Rossana Sapiro. This project evolved, and eventually when the call for Expanding Global Access opened, we put together part of what IMAGINA’s goals were, and we added a few other things. Essentially, we kept the components of training human resources, the train-the-trainer program, our introductory course on Fundamentals of Bioimaging Processing, and we added a postdoc. We trained local students and we put together an advanced course in the area of deep learning for bioimaging. This was in 2020 or 2021, and now we are putting together a course in AI – it’s an area that has expanded so much and is so essential! How did CZI help? It helped me in forcing me to envisage and plan what IMAGINA would become in the short and long term future. It also helped me in finding a community. Many of the people I interact with now belong to the CZI community too. Before CZI I knew some collaborators by name, in Mexico, Argentina, Chile, etc. But now we are great colleagues. We have spent a lot of time together at CZI meetings and in other networks too. So I am really grateful not only for the funding to develop our research, hire people and allow mobility, but also for finding a community that has the same interests as me. It also allows us to move people in the region: we send students to learn things within the region, we bring visitors from the region, strengthening the region.

What are the biggest challenges you have faced during the implementation of your project, and in expanding access?

IMAGINA has an interesting banner: microscopy is a place where many disciplines converge. Many of us here come from different backgrounds, but we converge in the area of microscopy. One of my biggest challenges from IMAGINA in 2015 was to understand the community and make myself understood, from my applied mathematics/ computational/ machine learning background. To meet and figure out what each of us could contribute. This was achieved only through conversations, attending conferences and meetings, inviting others to give talks, and starting “to survive” in the talks of biologists! The other challenge, which is a bit related, was to really become part of the community. To fully integrate. I wouldn’t say it’s a closed community, but everyone knows each other. To arrive as a non-student, non-visiting professor, but from within their own academic community in the same country, but from a different area, wanting to do new things in this area (biology) was challenging. And then there have been challenges associated to the discipline in which I work. Getting students isn’t as easy as it is in Biology. The students in the engineering disciplines currently have a lot more job opportunities, and much better paid than in the academy. So it’s difficult to compete. Getting students who will stably stay in the scientific career, 2 years as a MSc and 4-5 years in the PhD is very complicated. To get undergraduate students is not so complicated because they have an obligatory undergraduate project during their degree so when I start telling them about what we do, bioimaging and biomedicine is attractive to them, and they join. But to retain those people is very hard. The area is very competitive, and we are competing with industry too. Industry pays a lot better in the area of engineering and now the area of artificial intelligence has made a big explosion.

Have you considered joining forces with industry, like joined fellowships with Google or other industry partners?

We have some partnerships for general areas of teaching in ML, but I haven’t secured anything like this for the area of bioimaging. In Uruguay the community from engineering, applied maths or computer science in bioimaging is really small. Essentially, they’re sales representatives of companies that sell things. There is no place for generating this type of fellowship. The region allows me to expand this, but I just haven’t explored this option thoroughly. Also there’s a way for presenting projects whereby the application is bioimaging, but where we would really develop research is on the fundamentals of machine learning. We could propose something like this. But I’d love to focus more on bioimaging to have more contact with the specific challenges of my collaborators from the area of life sciences. Sometimes one has to find how we can best support them from the basic science part, in a way that it has an impact on the applied questions. We have done it, but it’s a challenge. I have my own research line at a different level, and these projects arise from the interaction with others.

You applied to the call of expanding global access. I think access has a lot of meanings. It includes bridging disciplines. This grant is allowing you to bridge a gap in expertise. How do you see this happening?

I sometimes ask people ‘what colour are the nuclei in cells?’ and they tell me ‘blue’. It’s not correct. We first have to understand what it is that images are showing. So there is a lot of fake things we see in images (artefacts), and there is confirmation bias – the idea of ‘I think this is like so and so, I see an image that confirms it, and so I am sure it is like this’. But this is not enough. Regarding bridging gaps, this is necessary not only within the community but also expanding expertise from the academic scientific community to other areas, for example basic education: going to schools, holding open doors events at the institutes. In some events, our IMAGINA group provides a computer and a microscope, and we show coins, hairs, leaves, ants, cells, etc. Kids approach with a lot of interest, and of course, behind them comes their family. We show the screen of cell phones and we show how pixels look, and how colour is formed. Microscopy allows us to talk about all the disciplines around us and this creates a bridge – it breaks barriers. Obviously this also has allowed me to approach these other disciplines that need great input from a basic level. For example, if I have to think of an icon to symbolize science, there are 3 or 4 options: Einstein’s picture, an atom, the DNA helix, or a microscope. Generally, when we think of biology, the icon of choice is indeed the microscope. This summary in one figure says a lot. We should exploit this as an access to the various other disciplines. It’s a way to attract young children and teenagers to learn about the scientific method, about science, and ask how the world works, and find a means to answer those questions through experimentation, which happens very naturally in children. We show them experimentation with a device that augments our capacities. This is also something that has allowed me to potentiate the grant and the community. Because what our Chilean and Mexican colleagues are under those same lines. We have a critical mass in Uruguay which is not big enough to deploy things in the same way as the other countries do. 

How did you decide to apply to the CZI program? How did you first hear about it?

I found out via email. At initially I thought ‘No, I can’t apply to this, it’s too big for me’. I thought about the funds – this is equivalent to five times the funding from any normal project in Uruguay. But then chatting with the co-head of IMAGINA, Rossana Sapiro, we realized that our work was a good fit. It forced us to make a plan on something we already had ongoing and in mind, and we realized that plan made sense. So we convinced ourselves that it was worth taking the chance to apply. It was a nice surprise when we learned we got the award. There are still challenges also because of the region in which we work. For example, I advertised the call for a postdoc and nobody applied. Nobody wants to go to Uruguay, except Uruguayans. So even though we distributed through the networks in BINA, LABI, etc, and it still didn’t work. I think there’s still not a lot of enthusiasm from mathematicians and computer sciences to join bioimaging and bioimage analysis. People in applied maths usually go to other areas of applied maths. That’s something for me to also learn how to do better: how to disseminate what we do within my own discipline. Maybe that’s more like a bridge to the inside of the discipline. 

Beyond funding, what else has CZI enabled you to do, which you couldn’t do before? 

The community for sure. Funds are essential but the community is even more important. I went to San Francisco in July. In that event we met many people, more than LABI or BINA, it’s worldwide so we get acquainted with other people and hear about other experiences. Communities are a network so it’s all bidirectional. Another benefit from the CZI grant was local visibility. When our projects were awarded the funding, we were in the national news: ‘Uruguayan scientists are financed for CZI’. It’s good for internal visibility to show that we have the capacity to compete within the global community, beyond our country’s borders. It’s known that science in many countries in Latin America is actually really good. This is a reinforcement or a confirmation of our capacities, even at an international environment. Science is fundamental for progress and for international integration. It’s good to show that we are recognized internationally, through projects like this one. 

How do you define democratization of microscopy? 

Democratization of microscopy: I think microscopy is a tool to attract the general population to science, to awaken interest for science and to recognize the role that science plays. That’s part of democratization: paving the way so that people can reach science as a whole. Microscopy helps doing so. It’s visual – which is fantastic for talks. You start with an image, and we are visual creatures. Democratization means making us equal, and equating means that one gives similar tools to all the people. We bring forward knowledge to people who would have otherwise not had access. That’s one of the possible ways of democratization. 

What future directions do you see in the project, and what’s the role of CZI in the future of your project and in the bigger picture?

Generally, research lines are defined, and from there we move around those lines. Community is the most important. I will be able to get other funding to invite people and move people, but the community is the strongest thing we have achieved, especially regionally: Chileans, Argentinians, Brazilians, Colombians, Mexicans are those with whom I engage the most with through CZI events. It’s a young community that decided to make its research lines in Latin America, so we will still be united. It also opened my eyes to see how others do research or how to do other things, from facing similar challenges in our region. CZI is allowing us to develop science in the region. I think CZI does fantastic things, they send the question back to us: they ask us what we as a community need, and based on that they make decisions on the direction of what to support or what program to generate. They listen to the community, and then take action to address these needs. So you see it, you feel the support. You know they listen to you, and they worry about addressing our needs. I am very grateful because we all have had the experience of speaking with other funders, expressing our needs, and nothing happens; they continue in the line they always have been and one feels ignored and undervalued. It’s nice to have the chance to be heard and maybe influence the policies of investment that CZI has. 

Check out our introductory post, with links to the other interviews here

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