https://www.oulu.fi/en/tissue-analysis-course-2023
DP00AL85-3001, 1-3 ECTS
Time: 17.3. - 23.3.2023
Place: Kontinkangas Campus
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)
Teaching language: English
Course enrolment: Registration via Peppi by
24th February 2023, course code: DP00AL85-3001
Acceptance: 12 participants (incl. demonstrations, practical work and exercises) selected
on account of a motivation letter
Evaluation criteria: Passed/failed according to participation in lectures and demonstrations,
carrying out practical work and exercises, providing feedback
Organizers: Biocenter Oulu, Biobank Borealis of Northern Finland and Research Units of Translational
Medicine and Clinical Medicine
Contact information: anne.heikkinen(at)oulu.fi, reetta.vuolteenaho(at)oulu.fi, Biocenter
Oulu Transgenic and Tissue Phenotyping Core Facility (BCO TTP Core), tel: +358-(0)294 486 133
Programme:
Friday 17th March, 2023
Lecture room 337B/338B, lectures*
8:00-8:15
Introduction to the course*
8:15-9:15
Mouse as a model for human diseases*
Reetta Hinttala, BCO TTP Core and RU of Clinical Medicine
9:15-9:30
Coffee break
9:30-10:30
From tissue to biomedical sample*
Anne Heikkinen, BCO TTP Core
10:30-11:00
Introduction to mouse necropsy*
Miia Salo, BCO TTP Core
Histology Lab 479B, practical work
11:00-11:30
Printing of tissue cassettes
TTP Core personnel
11:30-12:15
Lunch break, after which gathering in the Kieppi lobby
Oulu Laboratory Animal Centre
12:15-16:00 Mouse necropsy
Miia Salo and Anne Heikkinen, BCO TTP Core
Monday 20th March, 2023
Histology Lab 479B, practical work
8:00-9:15
Paraffin embedding
Objective slide printing
TTP Core personnel
Seminar room 487B, lecture*
9:15-10:45
Sample preparation for electron microscopy*
Introduction to the Electron Microscopy Image Library*
Ilkka Miinalainen, BCO EM Core
10:45-11:30 Lunch break
Histology Lab 479B, practical work
11:30-16:00
Paraffin block sectioning
Cryo sectioning
Manual HE staining of cryo sections
Whole mount sample preparation
BCO TTP Core personnel
Tuesday 21st March, 2023
Histology Lab 479B, demonstration
8:00-9:00
Automated HE staining
BCO TTP Core personnel
Lecture room P107, lecture
9:00-10:00
Common histological staining methods and artefacts
Markus Mäkinen, RU of Translational Medicine
10:00-10:15
Coffee break
10:15-11:15
Basic histological structures and findings
Markus Mäkinen, RU of Translational Medicine
Histology Lab 479B, demonstration
11:15-11:45
Automated slide cover slipping
TTP Core personnel
11:45-12:30
Lunch break
Lecture room P107, 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
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 22nd March, 2023
Independent studies
Familiarizing with preannounced web pages, such as EM Library
Familiarizing with and preparing for QuPath image analysis exercises
Thursday 23rd March, 2023
Histology Lab 479B, demonstration/practical work
8:00-9:00
Microscopy of histological slides
Veli-Pekka Ronkainen, BCO LM Core
Automated slide scanning
TTP Core personnel
Computer class 286A/286B, lecture*
9:00-10:00
Basics in image analysis*
Veli-Pekka Ronkainen, BCO LM Core
10:00-10:15
Coffee break
10:15-11:15
Prospects of the open-access QuPath image analysis tool*
Juha Väyrynen, RU of Translational Medicine
11:15-12:00
Lunch break
12:00-13:00
The Visiopharm image analysis software features*
Anne Heikkinen, BCO TTP Core
Computer class 286A/286B, practical work/demonstration
13:00-16:00
Exercises with QuPath
Juha Väyrynen and Sanna Palosaari, RU of Translational Medicine
Demonstration on the Visiopharm software working principles
Anne Heikkinen and Miia Salo, BCO TTP Core
Best wishes,
Mirja
------------------------------------------------------------------------------------------------------
Mirja Peltola, PhD, BSc (Tech.)
Koordinaattori | Coordinator
Oulun yliopisto | University of Oulu
Terveys- ja biotieteiden tohtoriohjelma | Health and Biosciences Doctoral
Programme
Tel. 0294 48 5447
PO Box 5000, FI-90014 OULUN YLIOPISTO
(Aapistie 5A, Room 476B)
www:
Terveys- ja biotieteiden tohtoriohjelma | Health and Biosciences Doctoral Programme