A collection of datasets, interactive web tools, learning materials, and open-source repositories produced and maintained for teaching and research.

Datasets & Research Data

UroCell Dataset

Volumetric data obtained with Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and corresponding high-resolution ground truth labels for cell organelles including mitochondria, endolysosomes, and Golgi apparatus. Used to train and benchmark deep learning models for cellular organelle segmentation.

  1. Zerovnik Mekuc, M., Bohak, C., Hudoklin, S., Kim, B.H., Romih, R., Kim, M.Y., & Marolt, M. (2020). Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data. Comput. Biol. Medicine, 119, 103693.
    PDF DOI 
    @article{DBLP:journals/cbm/MekucBHKRKM20,
  author = {Manca Zerovnik Mekuc and Ciril Bohak and Samo Hudoklin and Byeong Hak Kim and Rok Romih and Min Young Kim and Matija Marolt},
  title = {Automatic segmentation of mitochondria and endolysosomes in volumetric electron microscopy data},
  journal = {Comput. Biol. Medicine},
  volume = {119},
  pages = {103693},
  year = {2020},
  url = {https://doi.org/10.1016/j.compbiomed.2020.103693},
  doi = {10.1016/j.compbiomed.2020.103693},
  pdf = {https://lgm.fri.uni-lj.si/wp-content/uploads/2022/06/1538555331.pdf},
}
  2. Zerovnik Mekuc, M., Bohak, C., Bones, E., Hudoklin, S., Romih, R., & Marolt, M. (2022). Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data. Comput. Methods Programs Biomed., 223, 106959.
    PDF DOI 
    @article{DBLP:journals/cmpb/MekucBBHRM22,
  author = {Manca Zerovnik Mekuc and Ciril Bohak and Eva Bones and Samo Hudoklin and Rok Romih and Matija Marolt},
  title = {Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data},
  journal = {Comput. Methods Programs Biomed.},
  volume = {223},
  pages = {106959},
  year = {2022},
  url = {https://doi.org/10.1016/j.cmpb.2022.106959},
  doi = {10.1016/j.cmpb.2022.106959},
  pdf = {https://lgm.fri.uni-lj.si/wp-content/uploads/2022/06/112962819.pdf},
}

Psychological Measures of E-Learning Self-Regulation (2020)

Data file and tables representing the main research survey on the effectiveness of different types of learning scaffolding on the self-regulation of e-learning.

  • Citation: Katja Depolli Steiner, Luka Komidar, Sonja Pečjak, Tina Pirc, Anja Podlesek, Melita Puklek Levpušček, Alenka Gril, Ciril Bohak, Alenka Kavčič, Žiga Lesar, Matija Marolt, Matevž Pesek, Bojana Boh Podgornik, Aleš Hladnik, Cirila Peklaj. Psihološke mere samoregulacije e-učenja, 2020 : glavna raziskava [podatkovna datoteka]. Ljubljana: Univerza v Ljubljani, Arhiv družboslovnih podatkov, 2023.
  • Project: J5-9437: “Effectiveness of different types of learning scaffolding in self-regulation of e-learning” (funded by ARRS/ARIS).
  • DOI: 10.17898/ADP_PMSEUG20_V1
DOI / ADP Link 
@misc{ADP_PMSEUG20_V1,
  author = {Depolli Steiner, Katja and Komidar, Luka and Pečjak, Sonja and Pirc, Tina and Podlesek, Anja and Puklek Levpušček, Melita and Gril, Alenka and Bohak, Ciril and Kavčič, Alenka and Lesar, Žiga and Marolt, Matija and Pesek, Matevž and Boh Podgornik, Bojana and Hladnik, Aleš and Peklaj, Cirila},
  title = {Psihološke mere samoregulacije e-učenja, 2020 : glavna raziskava [podatkovna datoteka]},
  year = {2023},
  publisher = {Ljubljana: Univerza v Ljubljani, Arhiv družboslovnih podatkov},
  doi = {10.17898/ADP_PMSEUG20_V1},
  url = {https://doi.org/10.17898/ADP_PMSEUG20_V1}
}

Testing of Instruments for Determining Individual Differences in Self-Regulation of Learning (2019)

Pilot study dataset investigating individual differences and instrumentation for e-learning self-regulation evaluation.

  • Citation: Katja Depolli Steiner, Luka Komidar, Sonja Pečjak, Tina Pirc, Anja Podlesek, Melita Puklek Levpušček, Alenka Gril, Ciril Bohak, Alenka Kavčič, Žiga Lesar, Matija Marolt, Matevž Pesek, Bojana Boh Podgornik, Aleš Hladnik, Cirila Peklaj, et al. Preverjanje instrumentov za ugotavljanje individualnih razlik pri samoregulaciji učenja, 2019 : pilotna raziskava [podatkovna datoteka]. Ljubljana: Fakulteta za družbene vede, Arhiv družboslovnih podatkov, 2022.
  • Project: J5-9437: “Effectiveness of different types of learning scaffolding in self-regulation of e-learning” (funded by ARRS/ARIS).
  • DOI: 10.17898/ADP_IRSUP19_V1
DOI / ADP Link 
@misc{ADP_IRSUP19_V1,
  author = {Depolli Steiner, Katja and Komidar, Luka and Pečjak, Sonja and Pirc, Tina and Podlesek, Anja and Puklek Levpušček, Melita and Gril, Alenka and Bohak, Ciril and Kavčič, Alenka and Lesar, Žiga and Marolt, Matija and Pesek, Matevž and Boh Podgornik, Bojana and Hladnik, Aleš and Peklaj, Cirila},
  title = {Preverjanje instrumentov za ugotavljanje individualnih razlik pri samoregulaciji učenja, 2019 : pilotna raziskava [podatkovna datoteka]},
  year = {2022},
  publisher = {Ljubljana: Fakulteta za družbene vede, Arhiv družboslovnih podatkov},
  doi = {10.17898/ADP_IRSUP19_V1},
  url = {https://doi.org/10.17898/ADP_IRSUP19_V1}
}

Probabilistic Segmentation of Folk Music Recordings - Dataset (MPiE)

A benchmark dataset built to evaluate probabilistic segmentation methods on field recordings of Slovenian folk music.

  • Associated Publication: Ciril Bohak, Gregor Strle, Matija Marolt. Probabilistic segmentation of folk music recordings - dataset (MPiE). Ljubljana: Fakulteta za računalništvo in informatiko, 2016.
Website Link 
@misc{mpie_bohak_2016,
  author = {Bohak, Ciril and Strle, Gregor and Marolt, Matija},
  title = {Probabilistic segmentation of folk music recordings - dataset (MPiE)},
  year = {2016},
  publisher = {Ljubljana: Fakulteta za računalništvo in informatiko},
  url = {http://lgm.fri.uni-lj.si/ciril/mpie-bohak-2016/}
}

Transcription of Folk Music - Dataset (JAES)

Benchmark dataset used for folk music transcription research, containing annotated audio recordings of Slovene folk songs.

  • Associated Publication: Ciril Bohak, Gregor Strle, Matija Marolt. Transcription of folk music - dataset (JAES). Ljubljana: Fakulteta za računalništvo in informatiko, 2015.
Website Link 
@misc{jaes_bohak_2015,
  author = {Bohak, Ciril and Strle, Gregor and Marolt, Matija},
  title = {Transcription of folk music - dataset (JAES)},
  year = {2015},
  publisher = {Ljubljana: Fakulteta za računalništvo in informatiko},
  url = {http://lgm.fri.uni-lj.si/ciril/jaes-dataset/}
}

UterUS

Code and tools developed for automated segmentation and clinically-oriented measurement of uterine structures from 3D ultrasound data.

  • Code: GitHub Repository
  • Associated Publication: Gergolet, M., Nicolì, P., Vrtačnik-Bokal, E., Verdenik, I., Di Spiezio Sardo, A., Zizolfi, B., Xholly, A., Cagnacci, A., Scovazzi, U., Arena, A., Casadio, P., Sorgente, G., Gergolet, M., Boneš, E., Marolt, M., Lesar, Ž., Bohak, C., & others (2026). Defining the “normal uterus” by ultrasound measurement of uterine lengths, thicknesses, and angles in a population of nulliparous women : the normal uterus assessment study. Fertility and sterility, vol. 125(iss. 1), str. 127-136.
PDF DOI 
@article{COBISS.SI-ID:248313859,
  author = {Gergolet, Marco and Nicol\`{i}, Pierpaolo and Vrta\v{c}nik-Bokal, Eda and Verdenik, Ivan and Di Spiezio Sardo, Attilio and Zizolfi, Brunella and Xholly, Anjeza and Cagnacci, Angelo and Scovazzi, Umberto and Arena, Alessandro and Casadio, Paolo and Sorgente, Giuseppe and Gergolet, Martina and Bone\v{s}, Eva and Marolt, Matija and Lesar, \v{Z}iga and Bohak, Ciril},
  title = {Defining the ``normal uterus'' by ultrasound measurement of uterine lengths, thicknesses, and angles in a population of nulliparous women : the normal uterus assessment study},
  journal = {Fertility and sterility},
  year = {2026},
  volume = {vol. 125},
  number = {iss. 1},
  pages = {str. 127-136},
  doi = {10.1016/j.fertnstert.2025.07.1220},
}

Interactive Tools & Web Apps

Volumetric Path Tracing - VPT

Volumetric Path Tracing (VPT) is a physically based volume rendering application enabling interactive web-based exploration of volumetric data using ray tracing techniques directly inside standard web browsers on both desktop and mobile platforms.

  • Online Demo: VPT Live Demo

  • Code (WebGL 2.0 Original): GitHub Repository

  • Code (WebGPU Reimplementation): GitHub Repository (WebGPU reimplementation of the volumetric path tracer)

  • Code (Dimensionality Reduction & HDBSCAN Clustering): GitHub Repository

  • Code (Spectral Volume Rendering): GitHub Repository (associated publication: Diskretizirano spektralno upodabljanje volumetričnih podatkov)

  • Code (Continuous Spectral Volume Rendering): GitHub Repository (associated publication: Contiuous spectral volume rendering)

  • Code (Null-Collision Radiance Estimators): GitHub Repository (associated publication: Comparison of null-collision radiance estimators in light transport)

  • Associated Publications:

  1. Lesar, Z., Bohak, C., & Marolt, M. (2018). Real-time interactive platform-agnostic volumetric path tracing in webGL 2.0. In Proceedings of the 23rd International ACM Conference on 3D Web Technology, Web3D 2018, Pozna'n, Poland, June 20-22, 2018 (pp. 7:1--7:7).
    PDF DOI 
    @inproceedings{DBLP:conf/vrml/LesarBM18,
  author = {Ziga Lesar and Ciril Bohak and Matija Marolt},
  editor = {Krzysztof Walczak and Gabriel Zachmann and Jakub Flotynski and Kiyoshi Kiyokawa and Daniel Thalmann},
  title = {Real-time interactive platform-agnostic volumetric path tracing in webGL 2.0},
  booktitle = {Proceedings of the 23rd International ACM Conference on 3D Web Technology, Web3D 2018, Pozna\'n, Poland, June 20-22, 2018},
  pages = {7:1--7:7},
  publisher = {ACM},
  year = {2018},
  url = {https://doi.org/10.1145/3208806.3208814},
  doi = {10.1145/3208806.3208814},
  timestamp = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl = {https://dblp.org/rec/conf/vrml/LesarBM18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org},
  address = {New York},
  pdf = {https://lgm.fri.uni-lj.si/wp-content/uploads/2018/07/1537821891.pdf},
}
  2. Kurtagić, A., Marolt, M., Lesar, Ž., & Bohak, C. (2024). Contiuous spectral volume rendering. In Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26. - 27. september 2024 (pp. str. 411-414).
    PDF 
    @inproceedings{COBISS.SI-ID:209253379,
  author = {Kurtagić, Alen and Marolt, Matija and Lesar, Žiga and Bohak, Ciril},
  title = {Contiuous spectral volume rendering},
  booktitle = {Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26. - 27. september 2024},
  publisher = {Slovenska sekcija IEEE, Fakulteta za elektrotehniko},
  year = {2024},
  editor = {Žemva, Andrej and Trost, Andrej},
  series = {Zbornik ... Elektrotehniške in računalniške konference (Online), 33},
  pages = {str. 411-414},
  address = {Ljubljana},
}
  3. Jezeršek, J., Marolt, M., Lesar, Ž., & Bohak, C. (2024). Diskretizirano spektralno upodabljanje volumetričnih podatkov. In Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26. - 27. september 2024 (pp. str. 415-418).
    PDF 
    @inproceedings{COBISS.SI-ID:209249539,
  author = {Jezeršek, Jernej and Marolt, Matija and Lesar, Žiga and Bohak, Ciril},
  title = {Diskretizirano spektralno upodabljanje volumetričnih podatkov},
  booktitle = {Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26. - 27. september 2024},
  publisher = {Slovenska sekcija IEEE, Fakulteta za elektrotehniko},
  year = {2024},
  editor = {Žemva, Andrej and Trost, Andrej},
  series = {Zbornik ... Elektrotehniške in računalniške konference (Online), 33},
  pages = {str. 415-418},
  address = {Ljubljana},
}
  4. Colnar, B., Marolt, M., Bohak, C., & Lesar, Ž. (2024). Comparison of null-collision radiance estimators in light transport. In Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26. - 27. september 2024 (pp. str. 419-422).
    PDF 
    @inproceedings{COBISS.SI-ID:209246723,
  author = {Colnar, Brin and Marolt, Matija and Bohak, Ciril and Lesar, Žiga},
  title = {Comparison of null-collision radiance estimators in light transport},
  booktitle = {Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024 : Portorož, Slovenija, 26. - 27. september 2024},
  publisher = {Slovenska sekcija IEEE, Fakulteta za elektrotehniko},
  year = {2024},
  editor = {Žemva, Andrej and Trost, Andrej},
  series = {Zbornik ... Elektrotehniške in računalniške konference (Online), 33},
  pages = {str. 419-422},
  address = {Ljubljana},
}

VolWeb: WebGPU Volume Renderer

VolWeb is a WebGPU and WebAssembly (WASM) based volume renderer for visualizing multi-channel volumetric data. The rendering engine uses GPU ray casting combined with local ambient occlusion and soft shadows to achieve premium, real-time visualization directly in web browsers.

  • Online Demo: nano-oetzi-webgpu Demo
  • Code: GitHub Repository
  • Associated Publication: Nguyen, N., Bohak, C., Engel, D., Mindek, P., Strnad, O., Wonka, P., Li, S., Ropinski, T., & Viola, I. (2023). Finding Nano-Ötzi : cryo-electron tomography visualization guided by learned segmentation. IEEE transactions on visualization and computer graphics, vol. 29(no. 10), str. 4198-4214.
PDF DOI 
@article{COBISS.SI-ID:112947459,
  author = {Nguyen, Ngan and Bohak, Ciril and Engel, Dominik and Mindek, Peter and Strnad, Ond\v{r}ej and Wonka, Peter and Li, Sai and Ropinski, Timo and Viola, Ivan},
  title = {Finding Nano-\"{O}tzi : cryo-electron tomography visualization guided by learned segmentation},
  journal = {IEEE transactions on visualization and computer graphics},
  year = {2023},
  volume = {vol. 29},
  number = {no. 10},
  pages = {str. 4198-4214},
  doi = {10.1109/TVCG.2022.3186146},
}

Learning & Teaching Materials

3D Modeling with Blender (3D modeliranje z orodjem Blender)

Learning materials, exercises, and assets introducing students to 3D modeling, lighting, materials, and animation workflows using the open-source software Blender.

3D Modeling with Autodesk Maya (3D modeliranje z orodjem Autodesk Maya)

Comprehensive introduction and tutorials for Autodesk Maya, covering polygon modeling, animation, rigging, and rendering.

Open-Source Code & Software

RenderCore

RenderCore is a modern WebGPU-based 3D rendering engine built to power ROOT-EVE, enabling real-time visualization of high-energy physics event reconstructions in the browser.

  • Code: GitHub Repository
  • Associated Publication: Bohak, C., Kovalskyi, D., Linev, S., Mrak Tadel, A., Strban, S., Tadel, M., & Yagil, A. (2023). RenderCore – a new WebGPU-based rendering engine for ROOT-EVE. CoRR, abs/2312.11729, str. 1-8.
PDF DOI 
@inproceedings{COBISS.SI-ID:185884931,
  author = {Bohak, Ciril and Kovalskyi, Dmytro and Linev, Sergey and Mrak Tadel, Alja and Strban, Sebastien and Tadel, Matev\v{z} and Yagil, Avi},
  title = {RenderCore -- a new WebGPU-based rendering engine for ROOT-EVE},
  booktitle = {CHEP 2023 : 26 International Conference on Computing in High Energy \& Nuclear Physics : Norfolk, Virginia, USA, May 8-12, 2023},
  publisher = {Thomas Jefferson National Accelerator Facility},
  year = {2023},
  pages = {str. 1-8},
  address = {Newport News (VA)},
  journal = {CoRR},
  volume = {abs/2312.11729},
  url = {https://doi.org/10.48550/arXiv.2312.11729},
  doi = {10.48550/ARXIV.2312.11729},
}

NERVIS

NERVIS (Named Entity Relations Visualisation and Interaction System) is a web-based tool for graph-based exploration, visualization, and editing of named entities extracted from text documents.

  • Code: GitHub Repository
  • Associated Publication: Šmajdek, U. & Bohak, C. (2025). NERVIS : an interactive system for graph-based exploration and editing of named entities. CoRR, abs/2510.04971, str. 147-156.
PDF DOI 
@inproceedings{COBISS.SI-ID:267601923,
  author = {\v{S}majdek, Uro\v{s} and Bohak, Ciril},
  title = {NERVIS : an interactive system for graph-based exploration and editing of named entities},
  booktitle = {HCI SI Koper 2025 : proceedings of the 10th Human-Computer Interaction Slovenia Conference},
  publisher = {University of Primorska Press},
  year = {2025},
  pages = {str. 147-156},
  address = {Koper},
  doi = {10.26493/978-961-293-559-7.14},
  url = {https://doi.org/10.48550/arXiv.2510.04971},
}

WebGL Examples

A collection of web-based interactive examples demonstrating fundamental Computer Graphics concepts, shaders, and rendering techniques for students and developers.

Blocky Volume Package

Blocky Volume Package (BVP) is a web-friendly hierarchical volume data storage and compression format designed to enable quick streaming and direct ray-guided volume rendering in web browsers.

  • Code: GitHub Repository
  • Associated Publication: Lesar, Ž., Bohak, C., & Marolt, M. (2023). Blocky volume package : a web-friendly volume storage and compression solution. In WSCG 2023 : 31. International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision : proceedings (pp. str. 213-221).
PDF DOI 
@inproceedings{COBISS.SI-ID:159754755,
  author = {Lesar, \v{Z}iga and Bohak, Ciril and Marolt, Matija},
  title = {Blocky volume package : a web-friendly volume storage and compression solution},
  booktitle = {WSCG 2023 : 31. International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision : proceedings},
  publisher = {Vaclav Skala - UNION Agency},
  year = {2023},
  pages = {str. 213-221},
  address = {Plzen},
  doi = {10.24132/CSRN.3301.25},
}

NN-Based Volume Compression

A research repository evaluating the application of compressed neural network representation to volumetric datasets for efficient transmission and GPU decoding.

  • Code: GitHub Repository
  • Associated Publication: Kristan, A., Marolt, M., Bohak, C., & Lesar, Ž. (2024). Neural-network-based volume compression. In Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd ERK 2024 (pp. str. 452-455).
PDF 
@inproceedings{COBISS.SI-ID:209238275,
  author = {Kristan, An\v{z}e and Marolt, Matija and Bohak, Ciril and Lesar, \v{Z}iga},
  title = {Neural-network-based volume compression},
  booktitle = {Zbornik triintridesete mednarodne Elektrotehniške in računalniške konference ERK 2024 = Proceedings of the 33rd International Electrotechnical and Computer Science Conference ERK 2024},
  publisher = {Slovenska sekcija IEEE, Fakulteta za elektrotehniko},
  year = {2024},
  pages = {str. 452-455},
  address = {Ljubljana},
}

Laban Visualizer

A web-based dance visualiser based on Labanotation, ported to modern JavaScript. It visualizes dance movements described in Labanotation files.