PřF:Bi3307 Digital data processing - Course Information

Bi3307 Digital imaging data acquisition and processing in anthropology

Extent and Intensity

0/2/0. 2 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Petra Urbanová, Ph.D. (seminar tutor)
Mgr. Mikoláš Jurda, Ph.D. (seminar tutor)

Guaranteed by

doc. RNDr. Petra Urbanová, Ph.D.
Department of Anthropology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Petra Urbanová, Ph.D.
Supplier department: Department of Anthropology – Biology Section – Faculty of Science

Timetable

each odd Tuesday 9:00–12:50 FORLAB,-1021

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Anthropology (programme PřF, N-AN)
• Anthropology (programme PřF, N-ANT)

Course objectives

The course aims to present students with advanced recording and visualization techniques and their employment in the field of biological anthropology. In lab classes, students will be trained in processing 2D and 3D spatial digital data while being introduced to various computer programs for processing surface and volume 3D data. In addition, students will be trained in the employment of image and shape analysis software.

Learning outcomes

At the end of the course students will be able to:
- collect 3D spatial data of static as well as dynamic biological objects, such as bones or human body parts,
- process digital 2D and 3D data,
- analyze morphology of biological objects by means of geometric morphometrics,
- apply histomorphometric methods,
- comprehend the principles of traditional and advanced imaging techniques.

Syllabus

• Block 1
• 1) Theory of 3D data and surface digitalization, basics of MeshLab
• Digitalization via laser scanners and photogrammetry, 3D models, type of carried information, 3D formats, MeshLab basics - import and export of files, creation of thumbnails.
• 2) Editing digital 3D models, Blender and MeshLab
• Blender basics - import and export of files, data cleaning, filling of polygonal meshes, 3D sculpting (MeshLab and Blender). 3) Basics of analysis of 3D digital models, creation of outputs, 3D printing
• Measurement of direct and projective distances and digitalization of 3D coordinates (Meshlab and Blender), generation of images and animations, and 3D printing theory.
• 4) Seminar on block 1
• ------------------------------
• Block 2
• 5) 3D digitalization of living persons via optical scanners, analysis of digital models by the mesh-to-mesh comparison (FIDENTIS)
• Optical scanners (Vectra), texture editing and analysis, digitization of points based on texture, advanced mesh analysis (FIDENTIS).
• 6) 2D imaging and video recording
• Factors influencing the quality of photos and videos, file types, image analysis - distance measurement, point digitization.
• 7) Seminar on block 2
• -----------------------------
• Block 3
• 8) Volume scanning and ionizing radiation
• Theory of volume recording (MRI, CT), X-ray - basic principles of technologies, various types/variants of recording devices (whole-body/medical CT, dental CT, microCT) and examples of their outputs; volume data processing and evaluation, usability in anthropology and related fields.
• 9) Volume scanning processing
• Basics of work in selected non-commercial software - data preparation/preprocessing, basic 2D and 3D visualization options, manual and automatic segmentation, generation of three-dimensional models. Demonstration of processing and analysis options in the commercial program Avizo, examples of various segmentation strategies depending on the resolution and quality of data, type, size, and location of structures of interest.
• 10) Practical aspects of medical imaging devices
• 11) Seminar on block 3

Literature

required literature
• Urbanová P., Jurda, M., & Čuta, M. (2015). Záznam a analýza digitálních dat v antropologii. Brno: Masarykova univerzita. ISBN: 978-80-210-7754-6.

recommended literature
• Incrapera, A. K., Kau, C. H., English, J. D., McGrory, K., & Sarver, D. M. (2009). Soft Tissue Images from Cephalograms Compared With Those from a 3D Surface Acquisition System. The Angle Orthodontist. 80, 58–64.
• Kau, C. H. et al. (2007). Three-dimensional surface acquisition systems for the study of facial morphology and their application to maxillofacial surgery. International Journal of Medical Robotics and Computer Assisted Surgery. MRCAS 3, 97–110.
• Držík, M., Plecenik, A., Zahoran, M., Chlpik, J., Mach, Ľ., Bohunický, B., Varga, P., Gregor, M., & Anetta, M. (2008). Moderná mikroskopia a digitálne spracovanie obrazu. Skripta. Bratislava: FMFI UK. ISBN: 978-80-89186-37-2
• Nute, S. J., & Moss, J. P. (2000). Three-dimensional facial growth studied by optical surface scanning. The Journal Orthodontist. 27, 31–38.
• Moraes, C. A. de C., Dias, P. E. M., & Melani, R. F. H. (2014). Demonstration of protocol for computer-aided forensic facial reconstruction with free software and photogrammetry. Journal of Research in Dentistry. 2(1), 77– 90.
• Weber, G. W., Schäfer, K., Prossinger, H., Gunz, P., Mitteröcker, P., & Seidler, H. (2001). Virtual Anthropology: The Digital Evolution in Anthropological Sciences. Journal of Physiological Anthropology and Applied Human Science. 20, 69–80.
• Hillson, S. (2014). Tooth Development in Human Evolution and Bioarchaeology. Cambridge University Press.
• Hunt, E. E., & Hatch, J. W. (1981). The Estimation of Age at Death and Ages of Formation of Transverse Lines From Measurements of Human Long Bones. American Journal of Physical Anthropology. 54, 461–469.

Teaching methods

Lab classes taught in blocks for a limited number of graduate students enrolled in Anthropology Program seriously interested in the topic, in exceptional cases for students from other disciplines (by prior arrangement). The number of participants is limited by technical equipment (max. 10 students). Students work individually and in groups on a given practical task and process laboratory protocols under guidance of an instructor.

Assessment methods

During the semester, three partial tests will be administered, each at the beginning of one of the three seminars. The tests will focus on knowledge gained in previous lectures of the block. The tests will be conducted online via ROPOT in IS. Each test will consist of twenty multiple-choice questions, with 1-4 correct answers, focused on knowledge gained in previous lectures of the block. The test will be evaluated as follows: for the selected correct answers, the relative score will be added (0.25–1 point, depending on the number of correct answers in the given question). For each chosen wrong answer, one-third of a point will be subtracted. This means that one point for one question will be awarded only for selecting all the correct answers and only them. To pass the test, a gathering of 50 % points is necessary.
For each seminar, students will elaborate a protocol according to the assigned task.
To obtain the credit, it is necessary to actively participate in all three seminars, submit three elaborated protocols (or their corrected versions according to the teachers' comments), and pass all three continuous tests. The student has the right to one absence from the seminar and failure to pass one continuous test. In case of the absence, the credit will be awarded after passing the final oral exam. For the failed test, the student must pass the final test, consisting of 60 questions focused on the knowledge acquired during the whole semester. The type of questions, their scoring, and the limit for passing the final test will be the same as for the partial tests.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

• Enrolment Statistics (Spring 2023, recent)
  
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