Projects
Name
3D Reconstruction of the classical liver lobule
University
Turkey (TurkMSIC) - Baskent University, Ankara
Domain
Histology
Departement
Baskent University Faculty of Medicine Histology and Embryology Department, Baglica Campus, Dumlupinar Blv. 20. Km, 06810 Etimesgut/Ankara
Head
Fatma Helvacioglu, PHD
Tutor
Pinar Ayran Fidan, M.D.
Languages
Turkish, English
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No No Yes Yes No No No No
Type of Research Project
- Basic science
What is the background of the project?
Currently tools for 3D reconstruction are available as many people develop software available for both educational and therapeutically assistance purposes. We developed a specific software in our laboratory for the 3D reconstruction of any structure using serial sections of histological slides from organs of interest. This software also allows calculations and analysis of the area of interest. We also produce meshes to obtain a copy of the examined organ using a 3D printer. Having these samples helps both the students for educational purposes and also physicians or surgeons before any operation to be carried out on patient specific conditions. The Turkish Society of Histology and Embryology, founded in 1990, organizes annual meetings in order to further knowledge of its respective fields, and to strengthen the connections between other branches of science. It also aims to prevent malpractice of its respective fields. Furthermore, Baskent University Faculty of Medicine, Department of Histology and Embryology holds two separate laboratories for electron microscopy and light microscopy research. Electron microscope laboratory provides support to other units by examining samples under electron microscope as well as routine electron microscope service for the diagnosis of Baskent University Hospital. In addition to this, it has studies in the research projects of the state and other universities where the department is actively involved, using electron and advanced light microscope methods.
What is the aim of the project?
The structure of liver is described at section planes well enough but real 3D organization of the classical liver lobule is not defined in detail. Our aim is to determine the detailed 3D structure of the organ to obtain further evidence for its function
What techniques and methods are used?
Serial sections of liver will be uploaded into the Meshroom software, which then will automatically generate a 3-dimensional mesh of the liver. The mesh will be filled with architectural Computer Aided Design (CAD) programs specifically modified to replicate the crude histological properties of liver acini. Once the hexagonal acini are formed, another round of CAD programs will add details such as bile sinuii, portal and hepatic arterial circulatory lines and the central portal triads. In the final modelling phase we will work on the cytological characteristics of the lobule such as the placement of Kupfer and Stellate cells. The end result will be a near complete virtual reconstruction of a single liver lobule on both macroscopic and microscopic scales. All steps of the project will involve consultations from histologists and pathologists to stay as close to the in vivo microarchitecture as possible. We will use 3D modeling programs such as: 3D Slash. TinkerCAD FreeCAD SketchUP 123Design Blender Meshroom
What is the role of the student?
- The student will mainly observe
- The student will observe the practical experiments but will be highly involved in the analysis of the results
- If the project includes “lab work”
- the student will take active part in the practical aspect of the project
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
What are the tasks expected to be accomplished by the student? (Minimum 10 lines, provide detailed explanation) -The student will be required to improve their handling of lab equipment and biological tissue. -The student is required to know basic lab protocols for handling biological material, such as putting on sterile gloves. -The student will be expected to examine and interpret serial sections of the liver. -The student is expected to know the anatomy and functionality of the liver, as well as adjacent structures such as arteries and the gallbladder. -The student will learn how to use Meshroom to analyze the data obtained during the project. -The student will be expected to use his/her theoretical knowledge of histology of the liver to further enhance the interpretation of the sections.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
The student will be taught on how to use 3D modeling programs such as: 3D Slash. TinkerCAD FreeCAD SketchUP 123Design Blender Meshroom The softwares will be taught once a week depending on the availability of the tutors, Fatma Helvacioglu, PhD and Pinar Ayran Fidan, MD.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a scientific report
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
No specific skills are required.
Are there any legal limitations in the student’s involvement
No
Hours
6
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
Articles
- Korehisa;S.;Ikeda; T.; Okano; S.; Saeki; H.; Oki; E.; Oda; Y.; Hashizume; M. & Maehara Y.(2017) A novel histological examination with dynamic three-dimensional reconstruction from multiple immunohistochemically stained sections of a PD-L1-positive colon cancer. DOI: 10.1111/his.13400