Project Information

Description

VIVID-CELL Logo

Understanding the inner architecture of living cells is fundamental to biology and medicine, yet visualizing sub-cellular structures remains a major challenge. The VIVID-CELL project develops novel visualization methods that seamlessly merge real electron microscopy data with procedurally generated sub-cellular models, bridging two previously separate visualization domains.

Real volumetric data acquired with FIB-SEM microscopy reveals fine structural details of individual organelles, while procedural models — built from formal biological descriptions — enable flexible, multi-scale representations of complex intracellular environments. VIVID-CELL creates a unified framework where users can define which aspects of real and generated data are visualized and how they interact, supporting a broad visualization scale from individual organelles (nanometers) to multiple cells (micrometers).

The project focuses on developing visual models for key organelles including mitochondria, cytosol, the Golgi apparatus, lysosomes, and fusiform vesicles. These models are evaluated against state-of-the-art methods and validated using real bladder cell microscopy data. All developed methods target real-time performance within web browsers, leveraging physically-based rendering techniques such as path-tracing to deliver scientifically accurate and perceptually effective visualizations.

VIVID-CELL Visualization

Publications

  • Mena, O., Šmajdek, U., Zhang, W., Yu, P., Klein, T., Arold, S., Li, S., Viola, I., & Bohak, C. (2026). Coleborative online cryoET reconstruction, segmentation and visualization pipeline. In Visualizing biological data : VIZBI : the 16th International Meeting on Visualizing Biological Data : 14–17 April in Cambridge, UK (pp. str. 1).
  • Šmajdek, U., Boneš, E., & Bohak, C. (2025). GPU-based collocation visualization of immune niches in 3D cyclic immunofluorescence images. In Bio+MedVis Challenge @ IEEE VIS 2025 : November 2, 2025, [Vienna, Austria] (pp. str. 1-2).
  • Hudoklin, S., Humbel, B.M., Liang, F.X., Žerovnik Mekuč, M., Bohak, C., Marolt, M., Zaveršek, T., & Romih, R. (2025). Volume electron microscopy of intracellular compartments in the urinary bladder epithelium. In 17th Multinational Congress on Microscopy : 17MCM : Portorož, Slovenia, 7–12 September, 2025 : book of abstracts (pp. str. 154-155).
  • Drašček, M., Bohak, C., Marolt, M., & Lesar, Ž. (2025). Radiance probes for global illumination in volume rendering. In Proceedings of the 34th International Electrotechnical and Computer Science Conference ERK 2025 : Portorož, Slovenija, 25.–26. september 2025 (pp. str. 345-348).
  • Pristavnik Vrešnjak, M., Lesar, Ž., & Bohak, C. (2025). Pattern generation with neural cellular automata. In Proceedings of the 34th International Electrotechnical and Computer Science Conference ERK 2025 : Portorož, Slovenija, 25.–26. september 2025 (pp. str. 370-373).
  • Mažgon, E., Bohak, C., Marolt, M., & Lesar, Ž. (2025). Wood log reconstruction from Gaussian representations. In Proceedings of the 34th International Electrotechnical and Computer Science Conference ERK 2025 : Portorož, Slovenija, 25.–26. september 2025 (pp. str. 378-381).
  • Bulić, B. & Bohak, C. (2025). Learned laplacian-driven 3D mesh segmentation. In Proceedings of the 34th International Electrotechnical and Computer Science Conference ERK 2025 : Portorož, Slovenija, 25.–26. september 2025 (pp. str. 349-352).
  • Boneš, E., Khan, D., Bohak, C., Barad, B.A., Grotjahn, D.A., Viola, I., & Theußl, T. (2025). MidSurfer : a parameter-free approach for mid-surface extraction from segmented volumetric data. IEEE Computer Graphics and Applications, vol. 45(1). DOI: 10.1109/MCG.2025.3624572
  • Colnar, B., Marolt, M., Bohak, C., & Lesar, Ž. (2024). Comparison of null-collision radiance estimators in light transport. In Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26.–27. september 2024 (pp. str. 419-422).
  • Kurtagić, A., Marolt, M., Lesar, Ž., & Bohak, C. (2024). Continuous spectral volume rendering. In Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26.–27. september 2024 (pp. str. 411-414).
  • Jezeršek, J., Marolt, M., Lesar, Ž., & Bohak, C. (2024). Diskretizirano spektralno upodabljanje volumetričnih podatkov. In Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26.–27. september 2024 (pp. str. 415-418).
  • Kristan, A., Marolt, M., Bohak, C., & Lesar, Ž. (2024). Neural-network-based volume compression. In Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26.–27. september 2024 (pp. str. 452-455).