NO.212 Colors and visualization strategies in structural and cellular biology

Shonan Village Center

May 12 - 16, 2025 (Check-in: May 11, 2025 )


  • Monica Zoppè
    • CNR of Italy, Milan
  • Daisuke Inoue
    • Kyushu University, Japan
  • Yoshie Kiritani
    • Chiba University, Japan


Description of the workshop


Images of biological entities, from single molecules to whole cells, are increasingly used both in research and in media aimed at the public. Although the objects of such images are inherently colorless, in most cases colors are introduced, either as markers of specific features, or with purely aesthetic intent.

The results are often pleasing, sometimes spectacular. However, we wonder if colors could not be used also as achannel to deliver additional information to viewers, if they were used in a consistent manner, while still obtaining beautiful images.

The community concerned with the notion of 'molecular graphics' includes professionals from a variety of fields, including cell and structural biology, bio-informatics, physics, computer graphics, and art. In a recent workshop (, it has emerged that developing a set of guidelines for the use of color, as proposed by one of the organizers, could help both creators and viewers.

Accordingly, we propose to host a special workshop that will gather a very diverse group of experts to focus on the exchange of expertise and ideas and on the collaboration towards the common aim of introducing meaningful colors in the representation of small scale biology. Such result would imply that the computational tools commonly used for structural and cellular studies introduce algorithmic mechanisms for dealing with colors or other visual clues. An example of such research, resulting in the Mol* program, has been recently published by David Sehnal and Alexander Rose, which are among the invitees.


Based on these premises, we will invite:

-molecular graphics practitioners:from the pioneering work of Drew Berry (WEHI, Australia), the group of Art Olson, including Davide Goodsell (Scripps, SanDiego, USA) and Graham Johnson (now at Allen Institute, San Francisco, USA), Gael McGill (of Clarafi, Boston, USA) and myself MZ (Scientific Visualization Unit, Italy), all of which started > 15 years ago, today the art and science of Molecular Graphics (or Nanoscopic Visualization or Cellular Animation…) has become much easier, and quite popular, with possibly hundreds of practitioners. We will invite several of the best known and most creative young and older MolGraphers, also including, for example, Brady Johnston, Ryo Mizuta and Matthew Clark, who are world-famous students or young researcher of molecular graphics, as demonstrated by the sheernumber of their followers on social media Brady: 13k followers, Ryo: 1.8k, Matthew: 3.6k followers.

-experts in visual communication, visual studies, history of art and science, and design theory:the science of colors has very many facets: from cultural relevance to perception, from emotional association to aesthetics. The inputof the ‘color and design’ community will be fundamental for setting the basis of a new color and visual code to be applied at the scale of the invisible.

-producers of the tools at the basis of imagery:from structure to microscope and EM segmentation, all tools make some use of colors to allow easy identification (by humans) of features related to the objects of study. If any agreement can be reached (as we believe it will), the participation of the people that produce and maintain these tools will be paramount, as it will have to be embedded as the default choice for the selected features.

-producers of the graphics tools:while many of the ‘discovery tools’ (above) can deal with the specific objects, typically characterizedby their size, the production of larger representations, such as short animations, Virtual and Augmented Reality tools, and other compositions, often span several orders of magnitude in dimension, from nanometers to tens of micrometers. These productions require the adoption of filmic graphics tools, of the kind typically developed for the entertainment industry of movies and games. However, these tools need special adaptations in order to accommodate molecular information and calculi. We will invite some of the producers of these dedicated versions of the 3D tools for special effects.Furthermore, the ‘translation’ of bioinformatics data into visual graphics implies the development of new informatic methods at the interface between biology and computer graphics.

-experts in biology teaching and education, including publishers of the major biological journals and textbooks:a new convention can make sense only if it is widely shared. Today youth first contact with the world of cells happens at school at very young age, and keeps returning during further studies, and also through the work of art. The recent pandemic made everyone familiar with the shape of the virus SARS Co-V2, and it is easy to forecast that new diseases and new insights into their functioning will be communicated to the large public through visual imagery. In order for everyone to understand a common concept when viewing similar images, the underlying principle must be shared among those who help the transfer of information from the laboratory to the public, atall levels. For this reason we will invite editors and illustrators of the major biological journals dealing with biological science and with the science of education in biology.

The list of possible inviteesspans 13 different nationalities, from the 5 continents (although parts of the world some are not very well represented). We would appreciate the possibility of adding (or changing) some of the invites, in order to obtain a more diverse geographical and cultural distribution of participants.

Five days workshop

After a reciprocal presentation of expertise and presentation of the possible contributions by experts in the different disciplines, we intend to discuss:

-the possible basis for a more effective and meaningful use of color in image construction.

Day 1

-which concepts could be best described by artificial coloring or other visual features (places, forces, identity of components, status of reactions…).

Day 1-2

-which color features would be best suited to convey these concepts (based on perception, ease of use, implementation and identification).

Day 2-4

-how to implement a new color and visualization strategy.

Day 4-5

-how to evaluate its efficacy.

Expected Outcomes

These discussions will guide our future actions, possibly including a coordinated research proposal to be submitted to major funding agencies.

As mentioned above, the idea was presented at an earlier, more general workshop and has already met with general approval from the MolGraphers, a community in which two of the organizers (D.I. and M.Z.) are well established. MZ previously participated in the NII-Shonan meeting in 2018, during which we discussed a related topic: Web Molecular Graphics: Emerging Technologies & Standards.

In the meeting of this proposal, in which we will invite some of the participants to the earlier meeting, we intend to focus on a specific topic, that will contribute to the actuation of the ideas presented before, and also set a series of ‘basic principles’ that should apply to the general theme of cellular biology, informing the public at all levels, including occasional by-passers, primary to high school students and expert practitioners.

For this reason, besides gathering scholars and practitioners from various disciplines, we will make a special effort to include people from diverse backgrounds and cultural/geographic origins.

To facilitate the adoption and to help in the preparation of a major research project of global interest we will reach out to institutional and commercial groups that might be interested in participating and possibly sponsoring part of the workshop.

More specifically, we have in mind a set of specific short- and long-term outcomes:

  1. Agree that the task is important and that the time is ripe to address the issue. Very likely
  2. Agree on a selection of cellular concepts that can be displayed visually. Likely
  3. Consider different means of delivering visual information and select a range of possibilities. Likely
  4. Discuss the possible association of specific visual tools and communication strategies for different biological concepts. Possible/likely
  5. Decide to set up a larger initiative (e.g. a joint application for a collaborative grant) towards the goal of a ‘visual vocabulary’. Possible
  6. Consider possible participants, funding source, overall organization and timing of the project in point 5. Possible
  7. Prepare a draft white paper on the workshop discussion and its outcomes. Likely
  8. Propose future actions. Likely

From the perspective of bioinformatics, there are significant potential outcomes expected from this international workshop. In recent years, there have been efforts to visualize cells and biomolecules using technologies such as 2D/3D computer graphics and virtual reality (VR).

-Advancements in visualization technology:The discussions and knowledge sharing in the workshop could foster advancements in the visualization technology of cells and biomolecules. This can lead to more simple visual representations and interactive visual experiences for VR visualization tools, enhancing the understanding and interpretation of biological data in the field of bioinformatics.

-Integration of big data analysis and visualization: The analysis and visualization of big data are important topics in bioinformatics. The workshop could involve discussions on integrating the analysis and visualization of biological big data, potentially leading to the proposal of more effective methods for understanding patterns and relationships within biological data.

-Standardization of visualization data sharing and exchange: When multiple research groups or institutions use different visualization techniques, sharing and exchanging data can become challenging. The workshop may involve discussions on standardizing the sharing and exchange of visualization data. This could establish a framework for easily sharing and reusing data obtained through different visualization methods.

-Enhancement of usability and user experience: Withadvancements in visualization technology, it is crucial to make cellular and biomolecular data more user-friendly and intuitively understandable. The workshop could engage in discussions on improving usability and user experience of visualization tools, leading to the development and improvement of effective visualization techniques from a bioinformatics perspective.

By addressing these outcomes, the workshop aims to contribute to the field of bioinformatics by advancing the visualization of biology, enabling better comprehension and analysis of biological data.