When physics and biology collide

Collaborations between physicists and biologists can be tricky to negotiate, but a new microscopy method proves that they can also be very rewarding.

Cell biologist Isabel Palacios from Cambridge University and Queen Mary’s University, London, encountered a problem in 2015. She studies intracellular motion, using Drosophila oocytes as a model system, and was struggling to quantify and distinguish between the different types of motion occurring within the cells.

At about this time, Palacios attended a cross-disciplinary biophysical conference at the Lorentz center (a center for scientific workshops), where she attended a talk by a physicist, Fabio Giavazzi from the University of Milan. Giavazzi demonstrated an early version of a new image processing technique, differential dynamic microscopy (DDM), which extracted detailed quantitative data that described how bacteria move within a crowded, noisy environment.

“[The images presented] didn’t have a high resolution microscopy-wise, but they were still able to examine the motion of the bacteria in a lot of detail. I was quite impressed by that,” said Palacios.

Palacios wasted no time in approaching Giavazzi and his supervisor Roberto Cerbino to show them her time-lapse videos of live Drosophila oocytes. The pair thought they could help examine the varied motions of cytoplasmic components within the oocyte. “At that point the technique had never been used for intracellular motion,” said Palacios.

The scientists worked together to apply DDM to simultaneously study intracellular vesicles and the underlying actin mesh, and discovered a previously unidentified correlation between the two systems (1). “It worked beautifully! I was blown away by how much it can pick up and how relatively easy it could be done,” Palacios recalled.

The intersection between biology and physics isn’t easy for scientists from either discipline to navigate, yet DDM is the product of a successful collision between the two. However, implementing DDM in biological analysis still faces some math shaped obstacles and cross-disciplinary communication hurdles.

The Physical Discovery

“DDM is a quantitative microscopy technique that makes use of standard readily available microscopes,” said Cerbino. “This makes it very simple to implement, and it can be applied to a variety of systems, both for physicists and for biologists.”

Part of DDM’s attraction lies in its flexibility to extract data from movies taken on any type of microscope. This means that no new equipment needs to be purchased to extract statistically strong data from the noisy systems common within cells.

But how did Cerbino, a physicist, come to focus on a biological question?

Cerbino works in optics. While watching the movement of particles in a solution under a microscope one day, he wondered if there was any reason that a statistical calculation he was using to analyze X-ray scattering data couldn’t work with a microscope. An initial discussion with Fabio Giavazzi raised a series of problems, and Cerbino set the idea aside.

Then in August 2007, Cerbino was invited to Harvard to give a talk about his paper published in Nature Physics (2) that described this X-ray scattering analysis. “During my talk, my host, David Weitz, stood up and started criticizing everything I had said,” said Cerbino. After a bit of back and forth, Cerbino managed to address the opposing points. “He told me, ‘okay, if you are right, this thing also has to work with white light,’” said Cerbino. “That is what I wanted to do from the very beginning!”

Upon returning to Switzerland, Cerbino set up an experiment up with his colleague, Veronique Trappe, to try the analysis with white light on a microscope. “The experiment worked and it was the fastest paper in my life!” said Cerbino. “We took the data in one afternoon, wrote the paper in one week, and it was accepted really quickly ” (3). Cerbino treasures the positive comments from one of the reviewers. “He’s one of my gods.”

Spreading to Biology

Since that paper, Cerbino has encouraged biologists to use DDM by presenting at conferences and workshops such as the Lorentz workshop that Palacios attended. Other scientists have also applied the technique with success, some with Cerbino’s help and others independently.

A former colleague of Cerbino’s from Milan, Pietro Cicuta (now at Cambridge, UK), is a big fan of the technique, and often uses it to analyze video data in the varied projects conducted by his biophysics group. “We often care about things that are assembling, self-assembling, or are having a transition that impacts their dynamics. DDM is the right tool to monitor all these transitions,” said Cicuta. “The literature up to now has used other methods, but they don’t extract the same amount of information as DDM, and I think they are often noisier and generally more painful to use.”

Cicuta’s team built on DDM to make multi-DDM, which has been shown to identify the temporal and spatial coordination of motile cilia beating across many cells (4). “Cilia dynamics are very difficult to single out in video microscopy images,” he said.

As well as actively using the technique, Cicuta helps promote DDM. He teaches undergraduate students to use DDM in classes and summer workshops to ensure that as many people get exposed to it as possible. “I think more people should use it,” said Cicuta. “Many teams are just wasting their time segmenting images or trying to develop really complicated image filters when they should just use DDM.”

“Any laboratory can do it,” said Cerbino. “The degree of difficulty is mainly related to the software.”

Navigating the Mathematical Barrier

DDM calculates the difference between the light signals encoded in two images by separating these signals into their different frequencies using a Fourier transform. This transform makes DDM seem complex and can put biologists off.

Biologists also may be a bit skeptical about the practical applications of novel microscope techniques, especially when the approaches are mathematical. New techniques are approached cautiously until seen in practice or adopted more widely.

“Even simplified, it looks difficult; there is a lot of information, tools, different types of analysis, and jargon that is scary,” said Cerbino. However, Cerbino has found that once users are trained, they are able to use DDM easily. The ongoing questions he receives usually relate to new applications, rather than further understanding of the mathematical modelling. “You can also download software that does the analysis for you,” said Cerbino.

As a biophysicist, Cicuta claims that DDM is a better method than others. “It’s simpler in the sense that yes, there is this math and algorithm behind it which is computationally intensive, but for the user, there are no thresholds, no parameters to set, nothing to do,” said Cicuta. “So it’s very unbiased and simple to run. Once the code is there, you just have to run the images through the code.”

Although it can be daunting to pick up new tools, Palacios hasn’t looked back since collaborating with Cerbino and is now planning to use DDM to extend her work into mammalian oocytes. It can be challenging to communicate across fields and both sides need to use lay terms to explain their problems, goals, and solutions, in order to find the middle ground. Despite these challenges, Palacios anticipates her brainstorming sessions with the physicists.

“In general, I think that interacting with physicists and mathematicians is going to be necessary to fully understand developmental and cell biology,” said Palacios.