Tissue Analysis Course 2023

Tissue analysis course will introduce:
- 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, DP00AL85-3001, 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