Tissue Analysis Course
- Mouse dissection and sample collection for biomedical research
- Preparation of variety of biological samples
- Basics in histological methods and image analysis
- Infrastructure available at the Kontinkangas campus for tissue analysis
Content and programme
Tissue Analysis Course, DP00AL85-3003, 1-3 ECTS
Time: 15.3. – 21.3.2024
Organizers: Biocenter Oulu, Biobank Borealis of Northern Finland, Faculty of Medicine Laboratory Unit, Research Units of Translational Medicine and Clinical Medicine, and Health and Biosciences Doctoral Programme/University of Oulu Graduate School.
Target group: Doctoral students in the fields of Health and Biosciences, lectures open for all
Credits: 3 ECTS (participation to all lectures, demonstrations and exercises, providing feedback)/1 ECTS (participation to all lectures*, providing feedback)
Course enrollment: Registration via Peppi at the latest 23.2., course code: DP00AL85-3003
Acceptance into the course:
- Participation to demonstrations, practical work, and exercises: 2 ECTS. 12 participants selected on account of a motivation letter. In order to participate to exercises, all lectures must be also attended.
- Participation to all lectures: 1 ECTS. 30 participants are selected in the order of registration.
Evaluation criteria: Passed/failed according to participation in lectures and demonstrations, carrying out practical work and exercises, providing feedback
Contact information: anne.heikkinen(at)oulu.fi, Biocenter Oulu Transgenic and Tissue Phenotyping Core Facility (BCO TTP Core), tel: +358-(0)294 486 133
PRELIMINARY PROGRAMME
Friday 15th March, 2024, Theme - Mouse sample collection
Computer class 286A/B, lecture*
8:30-9:00 Introduction to the course
9:00-10:00 Mouse as a model for human diseases
Anniina Hiltunen, BCO TTP Core and RU of Clinical Medicine
10:00-10:15 Coffee break
10:15-11:15 From tissue to biomedical sample
Anne Heikkinen, BCO TTP Core
11:15-11:45 Introduction to mouse necropsy
Miia Salo, BCO TTP Core
Histology Lab 479B, practical work
11:45-12:15 Printing of tissue cassettes
TTP Core personnel
12:15-13:00 Lunch break, after which gathering in the Kieppi lobby
Oulu Laboratory Animal Centre, demonstration and practical work
13:00-16:00 Mouse necropsy
Miia Salo and Anne Heikkinen, BCO TTP Core
Monday 18th March, 2024, Theme - Biological sample preparation
Histology Lab 479B, practical work
8:30-9:45 Paraffin embedding, Objective slide printing
TTP Core personnel
9:45-10:00 Coffee break
Computer class 286A/B, lecture*
10:00-11:30 Sample preparation for electron microscopy, Introduction to the Electron Microscopy Image Library
Ilkka Miinalainen, BCO EM Core
11:30-12:15 Lunch break
Histology Lab 479B, practical work
12:15-16:15 Paraffin block sectioning, Cryo sectioning, Manual HE staining of cryo sections, Whole mount sample preparation
BCO TTP Core personnel
Tuesday 19th March, 2024, Theme - Sample Visualization
Histology Lab 479B, demonstration
8:30-9:00 Automated HE staining
BCO TTP Core personnel
Lecture hall F202, lecture*
9:15-10:15 Common histological staining methods and artefacts
Markus Mäkinen, RU of Translational Medicine
10:15-10:30 Coffee break
10:30-11:30 Histological structures and pathological findings
Markus Mäkinen, RU of Translational Medicine
Histology Lab 479B, demonstration
11:30-11:45 Automated slide cover slipping
TTP Core personnel
11:45-12:30 Lunch break
Computer class 286A/B, lecture*
12:30-13:30 Principles of IHC and In situ hybridization methods
Katja Porvari, Faculty of Medicine Laboratory Unit
13:30-14:00 Possibilities in utilizing Biobank samples in research
Raisa Serpi, Biobank Borealis of Northern Finland
14:00-14:15 Coffee break, after which gathering in the Kieppi lobby
Pathology Laboratory of the RU of Translational Medicine, demonstration
14:15-15:30 Tour through a Pathology Laboratory, Demonstration on automated IHC and In situ hybridization
Markus Mäkinen, RU of Translational Medicine and Katja Porvari, Faculty of Medicine Laboratory Unit
Wednesday 20th March, 2024, Theme - Preparing for image analysis
Histology Lab 479B, demonstration
9:00-10:00 Microscopy of histological slides
Veli-Pekka Ronkainen, BCO LM Core
Automated slide scanning and introduction to the NDPview software
TTP Core personnel
10:00-10:15 Coffee break
Computer class 286A/B, lecture*
10:15-11:15 Basics in image analysis
Veli-Pekka Ronkainen, BCO LM Core
11:15-12:15 Prospects of the open-access QuPath image analysis tool
Juha Väyrynen, RU of Translational Medicine
12:15-13:00 Lunch break
Computer class 286A/B, Instructions for full course participants
13:00-13:30 Introduction to QuPath image analysis exercises
Juha Väyrynen and Sanna Palosaari, RU of Translational Medicine
Computer class 286B, Independent work
13:30-16:00 Independent preparing for QuPath image analysis exercises
Thursday 21st March, 2024, Theme - Image analysis
Computer class 286B, independent work
9:00-12:00 Independent preparing for QuPath image analysis exercises
Computer class 286A/B, lecture*
12:00-13:00 The Visiopharm image analysis software features
Anne Heikkinen, BCO TTP Core
Computer class 286A/B and Histology Lab 479B, Exercises/demonstrations (including a coffee break when convenient)
13:00-16:00 Review of QuPath image analysis exercises
Juha Väyrynen and Sanna Palosaari, RU of Translational Medicine
Demonstration on the Visiopharm software working principles
Anne Heikkinen and Miia Salo, BCO TTP Core
