Ana J. García Sáez:
a researcher at the University of Tübingen’s Interfaculty Institute of Biochemistry.
cellular machineries for which she uses super-resolution microscopy.
Life, and therefore biology, are also subject to the laws of physics and chemistry, although often biological research is done at a level where this is kind of obviated.
I find it totally intriguing to learn how life has taken advantage of the laws of physics to bloom, how small chemical molecules are capable of working together to give rise to a living entity and to figure out what makes the difference between dead and living matter.
--Ana J. García Sáez.
Her lab recently developed ASAP, which stands for Automated Structures Analysis Program, or ASAP. It’s a software tool to automate the extraction of information from images captured with super-res microscopy and to help with detecting and classifying cellular structures and pulling out quantitative information.
Her paper in Nature Methods about ASAP is here. The Github link is here.
And here is a profile of her.
Ana J. García Sáez attended the University of València. During her PhD research in molecular biology she did a fellowship at the Technical University of Dresden. She returned to Dresden as a postdoctoral fellow. After positions at the German Cancer Research Center and the Max Planck Institute for Intelligent Systems, she joined the faculty of the University of Tübingen.
Here is a bit more about her from a conversation that took place after the above-mentioned profile was published. This is a slightly edited version of the exchange with her.
Vivien: You are a sports buff, so what sports did you do today? Ultimate Frisbee? Dancing?
Ana: I went for a run this morning in an urban forest next to my home. Now, in summer, it is amazing to pass under the trees with all green around.
Vivien: Now that the paper is out and the community responding to it, perhaps people have started to download your tool to try it. What makes you happy about the method and the reactions to it?
We have received good reactions from colleagues in the imaging field and with expertise in machine learning. The number of likes on Github is good so far, but based on past experience I guess it will take a bit longer until the community really gives it a try and comes back to us with feedback and suggestions. We will need to keep advertising :-).
We are very curious to see how the community will respond. It would be great if people would also find the software useful and helpful in their research, use it for purposes that perhaps we didn’t think of, or modify it and improve it so that it evolves with time. That would be awesome.
Vivien: John Danial tweeted “Suggestions to improving ASAP (spec. on more shape descriptors) are welcomed.” He was in your lab, now a fellow at the University of Cambridge. He co-developed ASAP with you. Any suggestions coming in yet?
Ana: He told me he hasn't received any scientific comments or suggestions as of yet -perhaps people haven't started using it or they did and found no need for other shape descriptors. I would not be surprised if the first suggestions to improve ASAP come from our own lab, as we progress with research and get new needs.
Vivien: You mentioned how you study cellular machineries with super-resolution microscopy, mainly stochastic optical reconstruction microscopy (STORM). Do you think of software development as fun, as a necessity, as a hindrance, a little of all, something else?
Ana: Perhaps as a little of all. It is first a hindrance because the lack of it delays data analysis and reaching conclusions that bring new biological knowledge. This makes it then a necessity, if one aims to do things properly and efficiently.
But once you get at it, the process of development is quite fun: one has to think how to find the best solutions to defined problems, how to make the software intuitive and user-friendly… One also has to think carefully under which conditions the software analysis is valid, where the limitations are… is it still useful then?
These reasons make software development an intellectually enjoyable exercise, at least for me, who doesn’t have to type the code. But I believe John also enjoyed the process greatly :-)
Vivien: You had to do a lot of manual classification by hand and you mentioned this took a while and was slow. How did you keep your lab happy in those moments and they were, if I understand correctly, long moments?
Ana: Well, this depends on personality. For some people, long manual analysis was bearable if they saw the reason for it, the research discovery at the end of the process.
For others, it was particularly tedious and I had more difficulty keeping motivation high, I have to admit. As I think about it, I guess I tried to keep task packages small, to ask the group members to combine the computer analysis with wet-lab work, to have them working on other projects where progress was faster…
The García Sáez lab on a hike.
Vivien Your mentor and collaborator Henning Walczak from University College London said that you are always brimming with ideas about applying physics to biology. What captivates you about this interplay between physics and biology? And how have you experienced his mentoring?
Ana: Life, and therefore biology, are also subject to the laws of physics and chemistry, although often biological research is done at a level where this is kind of obviated.
I find it totally intriguing to learn how life has taken advantage of the laws of physics to bloom, how small chemical molecules are capable to work together to give rise to a living entity and to figure out what makes the difference between dead and living matter.
I met Henning some years ago in a conference and we quickly clicked. He is fun and very clever and I felt comfortable talking to him.
He is also ahead of me in the scientific career business, so it was only natural to me to ask him for advice any time I had a question about career moves, grants, references… He lived in a different country, but somehow we managed to meet with certain regularity at conferences or we would call or email. Throughout these years, I can say he has been really helpful, also as I made decisions about aspects of my scientific career.
Vivien: In our previous conversation, you mentioned the tomatina festival in your hometown Buñol, a village near València in Spain. People in your lab might think you are cool, or forgive me, a little nuts, to participate in tomatina. Participating is likely fun but really messy. What did you like about it as a kid and what do you like about it as an adult?
Ana: That is a pretty accurate description: fun and really messy. It is difficult to describe how it is to participate… You get an adrenaline high, it’s kind of special to feel part of a huge crowd that is having fun, a fundamental type of fun.
It’s like a battle where the weapons are tomatoes - you throw tomatoes and you get tomatoes all over, but it is just fun, nobody is seriously hurt. You have a license to be messy for once and indeed it is typical to wear a white shirt and check how red it gets after the tomatina. A couple of hours later everything is crystal clear, the participants and the streets. And guess what we traditionally get for lunch at home, tomato salad!
The tomatina is not for kids, I started participating when I was a teenager. Nowadays there is also a special tomatina for kids on a different date somewhat smaller in scale with instructors and caretakers for the little ones. My kids have watched it with interest a few times, but so far they have been too shy to enter the tomato fight area.
Celebrating tomatoes at tomatina in Ana García Sáez's hometown of Buñol, a village near València, Spain.
Please sign in or register for FREE
If you are a registered user on Springer Nature Protocols and Methods Community, please sign in