Tissue Analysis Course 2023

Tissue Analysis Course,  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 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

Learning outcomes: 

• Mouse dissection and sample collection for biomedical research
• Preparation of variety of biological samplesBasics in histological methods and image analysis
• Infrastructure available at the Kontinkangas campus for tissue analysis

The course covers the following topics:

• Mouse as an animal model
• Mouse dissection and sample collection
• Histological sample preparation
• Cryo sample preparation
• Whole mount sample preparation
• Principles in electron microscopy sample preparation
• Manual and automated staining and embedding of histological samples
• Principles in selected histological staining methods
• Immunohistochemistry and in situ hybridization
• Introduction to a pathology laboratory
• Possibilities in utilizing Biobank samples in research
• Primary tissue structures in histology/pathology
• Microscopy and scanning of histological slides
• Basics in image analysis
• Introduction to QuPath image analysis software and exercises
• Introduction to Visiopharm image analysis software and practice

Teaching methods:

• Lectures
• Demonstrations
• Practical work and exercises
• Independent learning

Study material: Online material provided in Moodle

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