Master’s Research Project, 2023-2024

Human Organoids: Modeling Disease

The Master of Science in Biomedical Communications (MScBMC) Program requires all students to undertake a Master’s Research Project (MRP) focused on visual communication in science and/or medicine. My project aims to address the communication gap in understanding human organoids, which are simplified three-dimensional models of organs grown in a lab. Human organoids have shown huge potential to study organ development, model hereditary and acquired diseases, as well as to develop patient-specific drug screening.

In this project, I take on several roles including researcher, author, designer, 2D and 3D animator, and, most importantly, project manager. The result of this project is an animation designed for undergraduate biology students and the educated public, explaining what organoids are and their potential applications.

Committee Members

Derek Ng (Professor, Department of Biomedical Communications, University of Toronto)
Liliana Attisano (Professor, Principal Investigator, Department of Biochemistry, University of Toronto)

Format

A 4-5 minute video with a combination of 2D and 3D animation.

Tools

Milanote
Mendeley
Figma
Autodesk Maya
Pixologic ZBrush
Adobe After Effects
Adobe Premiere Pro

Project Initiation

I've gathered all relevant information about the project on one Miro board. This approach allows me to maintain a constant focus on the goal, even as it may evolve over time, and also provides a general bird's-eye view of the project. However, the first step is to research the topic.

Topic Research

Utilizing popular databases such as Web of Science and Scopus, along with other online resources, I conducted an extensive literature review and media audit to identify and address a visualization challenge. With constructive feedback from both peers and faculty, I drafted a research proposal outlining the goals, objectives, and methods to effectively tackle the identified problem space.

Animation Treatment

Based on the literature review and media audit, I drew up an outline for future animation which I refer to as the animation treatment. It is a concise (1-2 page) written overview describing the proposed film, offering a glimpse of its shape and atmosphere rather than providing exhaustive details.

Script Writing

The narration script serves as the backbone, determining the sequencing and timing of the film. It also serves as a rapid iteration tool before visual execution, aiding in the organization and refinement of ideas. My script included descriptions of action, voiceover, and transitions between shots.

Storyboard

Storyboards are important for pre-visualizing movement and composition in the final animation. At this stage, I supplemented the script with simple black-and-white (or minimal color) sketches for subsequent pitches and discussions with stakeholders. I chose to begin with major beats, maintaining an economy of shots, and then filled in the frames in between.

Animatic

Sequential presentation of storyboards accompanied by a VoiceOver:

Development of 3D Assets

The main objective of this project was to tell a clear, scientifically accurate story. I took advantage of a unique opportunity to observe every phase of organoid development firsthand. Regular visits to the lab allowed me to become acquainted with the team and the organoid production protocol. With the animation in mind, I gathered reference microscopy images, blueprints of laboratory equipment, and a series of photos. Below, I will share more details about two specific challenges I set for myself.

3D Neuron Model

I've always been fascinated by the intricate shapes of neurons and their surprising resemblance to trees. I decided to include a scene featuring them in the introduction of the animation. Inspired by the work of Newt Studios, and particularly Alexey Kashpersky, I began modeling using Zspheres. You can see the result below:

However, during a consultation, Professor Woolridge introduced me to his NeuronBuild Zbrush script. This script allowed me to select neurons from a centrally curated inventory of digitally reconstructed neurons and glia, all associated with peer-reviewed publications, and export them to Zbrush as wireframes. This streamlined the modeling process, significantly enhancing both speed and accuracy.

Before importing the model into Maya for further refinement, I decided to texture it using Adobe Substance 3D Painter, a program that was previously unfamiliar to me. The intuitive interface and logic similar to other Adobe products made this step both enjoyable and fast.

After importing the geometry and texture maps into Maya, I chose to enhance the scene's complexity using Maya's MASH networks. I incorporated small dendrites and extracellular vesicles. The finishing touches included lighting adjustments and subtle camera animations. I decided to manage everything else during post-production, including the movement of vesicles using Trapcode Particular.

Organoid Model

Another challenge I faced was the procedural creation of an organoid model. This allowed me to easily modify the cellular composition, the number and shape of ventricles, and the cell colors to illustrate various markers of interest. I referred to images similar to the tree photographs below, where dots of different colors indicate transcripts from different genes, imaged using Molecular Cartography (Resolve Biosciences):

Credit: Ivano Legnini, Agnieszka Rybak-Wolf, Max Delbrück Center

Still Frames Carousel from the Full Version of the Animation

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References:

Ayres, P., & Paas, F. (2007a). Making instructional animations more effective: A cognitive load approach. Applied Cognitive Psychology, 21, 811–820. https://doi.org/10.1002/acp.1351
Ayres, P., & Paas, F. (2007b). Making instructional animations more effective: A cognitive load approach. Applied Cognitive Psychology, 21(6), 695–700. https://doi.org/10.1002/acp.1343
de Jongh, D., Massey, E. K., Berishvili, E., Fonseca, L. M., Lebreton, F., Bellofatto, K., Bignard, J., Seissler, J., Buerck, L. W. van, Honarpisheh, M., Zhang, Y., Lei, Y., Pehl, M., Follenzi, A., Olgasi, C., Cucci, A., Borsotti, C., Assanelli, S., Piemonti, L., … Bunnik, E. M. (2022). Organoids: A systematic review of ethical issues. Stem Cell Research and Therapy, 13(1). BioMed Central Ltd. https://doi.org/10.1186/s13287-022-02950-9
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Eichmüller, O. L., & Knoblich, J. A. (2022). Human cerebral organoids — A new tool for clinical neurology research. Nature Reviews Neurology, 18(11), 661–680. https://doi.org/10.1038/s41582-022-00723-9
Halverson, K. L., Freyermuth, S. K., Siegel, M. A., & Clark, C. G. (2010). What undergraduates misunderstand about stem cell research. International Journal of Science Education, 32(17), 2253–2272. https://doi.org/10.1080/09500690903367344
Huk, T., Steinke, M., & Floto, C. (2010). The educational value of visual cues and 3D-representational format in a computer animation under restricted and realistic conditions. Instructional Science, 38(5), 455–469. https://doi.org/10.1007/s11251-009-9116-7
Ide, K., Matsuoka, N., & Fujita, M. (2021). Ethical aspects of brain organoid research in news reports: An exploratory descriptive analysis. Medicina (Lithuania), 57(6). https://doi.org/10.3390/medicina57060532
Kim, J., Koo, B. K., & Knoblich, J. A. (2020). Human organoids: Model systems for human biology and medicine. Nature Reviews Molecular Cell Biology, 21(10), 571–584. https://doi.org/10.1038/s41580-020-0259-3
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Ploetzner, R., Berney, S., & Bétrancourt, M. (2021). When learning from animations is more successful than learning from static pictures: Learning the specifics of change. Instructional Science, 49(4), 497–514. https://doi.org/10.1007/s11251-021-09541-w
Tang, X. Y., Wu, S., Wang, D., Chu, C., Hong, Y., Tao, M., Hu, H., Xu, M., Guo, X., & Liu, Y. (2022). Human organoids in basic research and clinical applications. Signal Transduction and Targeted Therapy, 7(1). Springer Nature. https://doi.org/10.1038/s41392-022-01024-9
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