Ciril Bohak - Academia.edu (original) (raw)

Papers by Ciril Bohak

The Visual Computer

We present a novel smart visibility system for visualizing crowded volumetric data containing man... more We present a novel smart visibility system for visualizing crowded volumetric data containing many object instances. The presented approach allows users to form groups of objects through membership predicates and to individually control the visibility of the instances in each group. Unlike previous smart visibility approaches, our approach controls the visibility on a per-instance basis and decides which instances are displayed or hidden based on the membership predicates and the current view. Thus, cluttered and dense volumes that are notoriously difficult to explore effectively are automatically sparsified so that the essential information is extracted and presented to the user. The proposed system is generic and can be easily integrated into existing volume rendering applications and applied to many different domains. We demonstrate the use of the volume conductor for visualizing fiber-reinforced polymers and intracellular organelle structures.

IEEE Transactions on Visualization and Computer Graphics

We present a novel framework for 3D tomographic reconstruction and visualization of tomograms fro... more We present a novel framework for 3D tomographic reconstruction and visualization of tomograms from noisy electron microscopy tilt-series. Our technique takes as an input aligned tilt-series from cryogenic electron microscopy and creates denoised 3D tomograms using a proximal jointly-optimized approach that iteratively performs reconstruction and denoising, relieving the users of the need to select appropriate denoising algorithms in the pre-reconstruction or post-reconstruction steps. The whole process is accelerated by exploiting parallelism on modern GPUs, and the results can be visualized immediately after the reconstruction using volume rendering tools incorporated in the framework. We show that our technique can be used with multiple combinations of reconstruction algorithms and regularizers, thanks to the flexibility provided by proximal algorithms. Additionally, the reconstruction framework is open-source and can be easily extended with additional reconstruction and denoising methods. Furthermore, our approach enables visualization of reconstruction error throughout the iterative process within the reconstructed tomogram and on projection planes of the input tilt-series. We evaluate our approach in comparison with state-of-the-art approaches and additionally show how our error visualization can be used for reconstruction evaluation.

Proceedings of the 23rd International ACM Conference on 3D Web Technology

Figure 1: Progressive reinement of a rendering of the bonsai dataset. The resolution of the datas... more Figure 1: Progressive reinement of a rendering of the bonsai dataset. The resolution of the dataset was 512×512×182, and the resolution of the internal frame bufers was 512×512. At 20 frames per second the irst image appeared on the screen in a fraction of a second, showing a recognizable shape. The last and most accurate image took 10 seconds to generate.

Uporabna informatika

The paper presents a user study comparing the performance and usability of different input device... more The paper presents a user study comparing the performance and usability of different input devices for precise manipulation of 3D objects: a regular mouse, a 3D mouse, and the gesture-based Leap Motion Controller. We show that the 3D mouse is well suited for the task, as it yielded the lowest rotation error rate and best overall usability, while tasks were completed as fast with the 3D mouse as with the regular mouse interface. The 3D mouse got an average System Usability Scale (SUS) score of 88.7, the regular mouse 72.4, while the Leap Motion Controller was barely suitable for the task with an average SUS score of 56.5. The study showed that users needed the most time to finish the tasks with the Leap Motion Controller and that its gestures were not as easy to learn as with the 3D mouse. This led us to conclude that the 3D mouse is currently the best input choice among the tested devices for 3D tasks that require both high precision, quick completion and a fast learning curve.

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E-gradiva in e-učbeniki si počasi utirajo pot v naše šole. Njihov pravi pomen se je pokazal tudi ... more E-gradiva in e-učbeniki si počasi utirajo pot v naše šole. Njihov pravi pomen se je pokazal tudi ob zadnji epidemiji, ko so bile šole zaprte, učenci pa večkrat prepuščeni sami sebi in angažiranosti svojih staršev. Za uspešno učenje z uporabo e-gradiv mora učenec uporabiti primerne strategije samoregulacije učenja, ki mu omogočajo, da doseže zastavljene učne cilje. Učencem s slabše razvitimi samoregulacijskimi spretnostmi lahko pri učenju pomaga umestitev učnih opor med vsebino obravnavane snovi. V članku je predstavljena pilotna raziskava na vzorcu 91 devetošolcev, v kateri smo preverjali delovanje učnih opor. V ta namen smo razvili e-učno okolje za prikaz učne enote z vstavljenimi različnimi vrstami učnih opor (kognitivne, metakognitivne in motivacijske), ki omogoča tudi beleženje aktivnosti učenca. Rezultati so pokazali, da so po ocenah učencev najboljša pomoč pri učenju kognitivne opore.

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Metoda sledenja potem je trenutni de facto standard za fotorealistično upodabljanje 3D prostorov... more Metoda sledenja potem je trenutni de facto standard za fotorealistično upodabljanje 3D prostorov zaradi svoje konceptualne in algoritmične enostavnosti. V zadnjih letih je bila uspešno uporabljena za upodabljanje prosojnih medijev in volumetričnih podatkov, a se njena širša uporaba ni prijela. Večina implementacij namreč za hitrejše doseganje rezultatov cilja na specifične platforme oz. strojno opremo, zato so posledično manj razširljive in zahtevnejše za namestitev. Kljub temu nam nedavne izboljšave na področju spletnih tehnologij omogočajo dostop do grafične strojne opreme iz spletnega brskalnika na platformno agnostičen način. V članku je predstavljena sodobna implementacija metode sledenja potem za volumetrične podatke, razvita v programskem jeziku JavaScript in s programskim vmesnikom WebGL 2.0. Rešitev podpira uporabo poljubnih 2D prenosnih funkcij in heterogenih volumetričnih podatkov, hkrati pa je interaktivna, platformno agnostična, enostavno razšir...

IEEE Transactions on Visualization and Computer Graphics, 2021

Immersive virtual reality environments are gaining popularity for studying and exploring crowded ... more Immersive virtual reality environments are gaining popularity for studying and exploring crowded three-dimensional structures. When reaching very high structural densities, the natural depiction of the scene produces impenetrable clutter and requires visibility and occlusion management strategies for exploration and orientation. Strategies developed to address the crowdedness in desktop applications, however, inhibit the feeling of immersion. They result in nonimmersive, desktop-style outside-in viewing in virtual reality. This article proposes Nanotilus-a new visibility and guidance approach for very dense environments that generates an endoscopic inside-out experience instead of outside-in viewing, preserving the immersive aspect of virtual reality. The approach consists of two novel, tightly coupled mechanisms that control scene sparsification simultaneously with camera path planning. The sparsification strategy is localized around the camera and is realized as a multi-scale, multi-shell, variety-preserving technique. When Nanotilus dives into the structures to capture internal details residing on multiple scales, it guides the camera using depth-based path planning. In addition to sparsification and path planning, we complete the tour generation with an animation controller, textual annotation, and text-to-visualization conversion. We demonstrate the generated guided tours on mesoscopic biological models-SARS-CoV-2 and HIV. We evaluate the Nanotilus experience with a baseline outside-in sparsification and navigational technique in a formal user study with 29 participants. While users can maintain a better overview using the outside-in sparsification, the study confirms our hypothesis that Nanotilus leads to stronger engagement and immersion.

As folk songs live largely through oral transmission, there usually is no standard form of a song... more As folk songs live largely through oral transmission, there usually is no standard form of a song-each performance of a folk song may be unique. Different interpretations of the same song are called song variants, all variants of a song belong to the same variant type. In the paper, we explore how various melody-based features relate to folk song variants. Specifically, we explore whether we can derive a melodic similarity measure that would correlate to variant types in the sense that it would measure songs belonging to the same variant type as more similar, in contrast to songs from different variant types. The measure would be useful for folk song retrieval based on variant types, classification of unknown tunes, as well as a measure of similarity between variant types. We experimented with a number of melodic features calculated from symbolic representations of folk song melodies and combined them into a melodybased folk song similarity measure. We evaluated the measure on the task of classifying an unknown melody into a set of existing variant types. We show that the proposed measure gives the correct variant type in the top 10 list for 68% of queries in our data set.

Sensors, 2020

Direct point-cloud visualisation is a common approach for visualising large datasets of aerial te... more Direct point-cloud visualisation is a common approach for visualising large datasets of aerial terrain LiDAR scans. However, because of the limitations of the acquisition technique, such visualisations often lack the desired visual appeal and quality, mostly because certain types of objects are incomplete or entirely missing (e.g., missing water surfaces, missing building walls and missing parts of the terrain). To improve the quality of direct LiDAR point-cloud rendering, we present a point-cloud processing pipeline that uses data fusion to augment the data with additional points on water surfaces, building walls and terrain through the use of vector maps of water surfaces and building outlines. In the last step of the pipeline, we also add colour information, and calculate point normals for illumination of individual points to make the final visualisation more visually appealing. We evaluate our approach on several parts of the Slovenian LiDAR dataset.

Lecture Notes in Computer Science, 2018

In this paper, we present a web-based system for visualization of flow simulation results in the ... more In this paper, we present a web-based system for visualization of flow simulation results in the vascular system for use with consumer-level hardware. The presented tool allows users to design, execute and visualize a flow simulation with a simple workflow on a desktop computer or a mobile device. The web interface allows users to select a vascular model, define the flow simulation parameters, execute the simulation, and interactively visualize the simulation results in real time using multiple visualization techniques. The server-side prepares the model for simulation and performs the simulation using SimVascular. To provide a more efficient transfer of the large amounts of simulation results to the web client, as well as reduce storage requirements on the server, we introduce a novel hybrid lossy compression method. The method uses an octree data subdivision approach combined with an iterative approach that regresses the data points to a B-Spline volume. The evaluation results show that our method achieves compression ratios of up to 5.7 for the tested examples at a given error rate, comparable to other approaches while specifically intended for visualization purposes.

Technologies for Optical Countermeasures XV, 2018

For detection of a small target using electro-optical systems, multi-band 2D image sensors are us... more For detection of a small target using electro-optical systems, multi-band 2D image sensors are used such as visible, NIR, MWIR, and LWIR. However, 2D imaging systems are not capable to detect a very small target and they are also not capable of calculating target 3D position coordinates to develop the strategic counter method. 3D sensors (e.g. Lidar, RGBD and stereo camera) are utilized to control unmanned vehicles for detecting threats and response for specific situations. Conventional Lidar systems are unable to detect small drone threat at distances higher than their maximum detecting range of 100 ∼ 120 meters. To overcome this limitation, laser radar (LADAR) systems are being developed, which allow the detection at distances up to 2 kilometers. In the development of LADAR, it is difficult to acquire datasets that contain cases of long distant targets. In this study, a fusion data generation with virtual targets technique based on minimum real LADAR initial map dataset is proposed, and precise small target detection method using voxel-based clustering and classification are studied. We present the process of data fusion generation and the experimental results for a small target detection. The presented approach also includes effective visualization of high-resolution 3D data and the results of small target detection in real time. This study is expected to contribute to the optimization of a drone threat detection system for various environments and characteristics.

$Research paper thumbnail of Finding Nano-\"Otzi: Semi-Supervised Volume Visualization for Cryo-Electron Tomography$

Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for... more Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural detail. Existing volume visualization methods, however, cannot cope with its very low signal-to-noise ratio. In order to design more powerful transfer functions, we propose to leverage soft segmentation as an explicit component of visualization for noisy volumes. Our technical realization is based on semi-supervised learning where we combine the advantages of two segmentation algorithms. A first weak segmentation algorithm provides good results for propagating sparse user provided labels to other voxels in the same volume. This weak segmentation algorithm is used to generate dense pseudo labels. A second powerful deep-learning based segmentation algorithm can learn from these pseudo labels to generalize the segmentation to other unseen volumes, a task that the weak segmentation algorithm fails at completely. The proposed volume visualization uses the deep-...

2018 41st International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2018

In this paper, we present a novel approach to integrating virtual reality (VR) into a web-based m... more In this paper, we present a novel approach to integrating virtual reality (VR) into a web-based medical visualization framework. The framework supports visualization of volumetric data, such as 3D scalar fields acquired by a CT, MRI or PET scanners. To improve users' perception, understanding and manipulation of 3D volumes, we adapted the traditional 2D screen representation with support for visualization of data in a VR environment. By providing complete visual immersion, VR can help users to gain better insights and understanding of the visualized data. Our main goal was to allow users to view the medical data in VR and interact with it with hand-held controllers for better immersion and spatial perception. In the paper, we present a novel approach to implementation of VR for medical imaging, which combines WebGL-based hardware accelerated web visualization with VR. This allows users to use the visualization framework with or without a VR headset by switching between "standard" and "VR" modes. Since visualization runs in a web browser, it is portable, easy to use on different devices and therefore accessible to a broad number of users. The visualization system was tested with real medical scans to assess its performance and usability.

Rasprave Instituta za hrvatski jezik i jezikoslovlje, 2020

The ability to process language data has become fundamental to the development of technologies in... more The ability to process language data has become fundamental to the development of technologies in various areas of human life in the digital world. The development of digitally readable linguistic resources, methods, and tools is, therefore, also a key challenge for the contemporary Slovene language. This challenge has been recognized in the Slovene language community both at the professional and state level and has been the subject of many activities over the past ten years, which will be presented in this paper. The idea of a comprehensive dictionary database covering all levels of linguistic description in modern Slovene, from the morphological and lexical levels to the syntactic level, has already formulated within the framework of the European Social Fund’s Communication in Slovene (2008-2013) project; the Slovene Lexical Database was also created within the framework of this project. Two goals were pursued in designing the Slovene Lexical Database (SLD): creating linguistic de...

In this paper we present a kiosk system designed for presentation purposes which bases on Kinect ... more In this paper we present a kiosk system designed for presentation purposes which bases on Kinect sensor technology as an input. The general idea is to create a platform for deploying presentations in predefined format for public screenings. The interaction with such system is crucial and is implemented with use of Microsoft Kinect sensor. While most kiosk systems are customized for end user purposes and need custom made content, we aim to create an uniform format of content packages that could be exchanged between different setups of presented system. Such packaging format also allows users to easily adapt the content of each individual system by only updating the web-pages included in the package. In presented system users can interact with content with gestures that are recognized by our system. Simple navigational gestures allow users to browse the content in nonlinear way, which results in better user experience.

V monografiji Slovar sodobne slovenscine: problemi in resitve so objavljeni rezultati raziskav, s... more V monografiji Slovar sodobne slovenscine: problemi in resitve so objavljeni rezultati raziskav, s katerimi so avtorji želeli odgovoriti na nekatera kljucna vprasanja pri snovanju koncepta sodobnega slovarja slovenskega jezika, ki bi bil kos izzivom sodobne leksikografije in bi (ponovno) umestil slovensko leksikografsko teorijo in prakso v mednarodni kontekst. Monografija prinasa 32 razprav, ki jih je prispevalo prav toliko avtorjev.

Fakulteta za računalništvo in informatiko Kataložni zapis o publikaciji (CIP) pripravili v Narodn... more Fakulteta za računalništvo in informatiko Kataložni zapis o publikaciji (CIP) pripravili v Narodni in univerzitetni knjižnici v Ljubljani COBISS.SI-ID=292758784

We present an assessment study of user experience and usability of different kinds of input devic... more We present an assessment study of user experience and usability of different kinds of input devices for view manipulation in a 3D data visualisation application. Three input devices were compared: a computer mouse, a 3D mouse with six degrees of freedom, and the Leap Motion Controller - a device for touchless interaction. Assessment of these devices was conducted using the System Usability Scale (SUS) methodology, with addition of application specific questions. To gain further insight into users' behaviour, the users' performance and feedback on the given tasks was recorded and analysed. The best results were achieved by using the 3D mouse (SUS score 88.7), followed by the regular mouse (SUS score 72.4). The Leap Motion Controller (SUS score 56.5) was the least preferred mode of interaction, nevertheless it was described as natural and intuitive, showing great potential.

New graphics APIs require users to implement a lot of needed functionality, such as memory manage... more New graphics APIs require users to implement a lot of needed functionality, such as memory management, by themselves. In this paper we present an abstraction layer build on top of such API, in our case the Vulkan API, for purpose of off-screen rendering of large data. We also present a use case for such abstraction layer implementation – a remote rendering system for simple Path Tracing accessible through web-based client-side application. The preliminary evaluation results show that implementation of simple Path Tracer is significantly faster then comparable implementation in OpenCL. In conclusion we also present possible extension and improvements of the developed abstraction layer.

The Visual Computer

IEEE Transactions on Visualization and Computer Graphics

Proceedings of the 23rd International ACM Conference on 3D Web Technology

Uporabna informatika

IEEE Transactions on Visualization and Computer Graphics, 2021

Sensors, 2020

Lecture Notes in Computer Science, 2018

Technologies for Optical Countermeasures XV, 2018

$Research paper thumbnail of Finding Nano-\"Otzi: Semi-Supervised Volume Visualization for Cryo-Electron Tomography$

2018 41st International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2018

Rasprave Instituta za hrvatski jezik i jezikoslovlje, 2020