Tissue Analysis Course

Friday 14th March, 2025, Theme - Mouse sample collection
286A/286B, lecture*
8:30-9:00 Introduction to the course (Anne Heikkinen, BCO TTP Core)
9:00-10:00 Mouse as a model for human diseases (Anniina Hiltunen, BCO TTP Core)
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, Anniina Hiltunen and Anne Heikkinen, BCO TTP Core) 

Monday 17th March, 2025, 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
286A/286B, lecture*
10:00-11:30 Ultrastructural phenotyping by electron microscopy (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 18th March, 2025, Theme - Sample Visualization
Histology Lab 479B, demonstration
8:30-9:00 Automated HE staining (BCO TTP Core personnel)
286A/286B, 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
286A/286B, 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 and OYS, demonstration
14:15-15:30 Tour through Pathology Laboratories, Demonstration on automated IHC and In situ hybridization (Markus Mäkinen, RU of Translational Medicine and Katja Porvari, Faculty of Medicine Laboratory Unit)
 
Wednesday 19th March, 2025, Theme - Preparing for image analysis
Histology Lab 479B, demonstration/independent work
9:00-10:00 Viewing of HE-stained slides (Miia Salo, Anniina Hiltunen and Anne Heikkinen, BCO TTP Core)
10:00-10:15 Coffee break
Histology Lab 479B, demonstration
10:15-11:30 Microscopy and imaging of histological slides (Veli-Pekka Ronkainen, BCO LM Core), Automated slide scanning and introduction to the NDPview software (TTP Core personnel)
11:30-12:15 Lunch break
286A/286B, lecture*
12:15-13:15 Basics in image analysis (Veli-Pekka Ronkainen, BCO LM Core)
13:15-14:15 Prospects of the open-access QuPath image analysis tool (Juha Väyrynen, RU of Translational Medicine)
14:15-14:30 Coffee break
286A/286B, Instructions for full course participants
14:30-15:00 Introduction to QuPath image analysis exercises (Juha Väyrynen and Sanna Palosaari, RU of Translational Medicine)
286A/286B, Independent work
15:00-16:00 Independent preparing for QuPath image analysis exercises

Thursday 20th March, 2025, Theme - Image analysis
286A/286B, independent work
9:00-12:00 Independent preparing for QuPath image analysis exercises
286A/286B, lecture*
12:00-13:00 The Visiopharm image analysis software features
286A/286B and Histology Lab 479B, Exercises/demonstrations (including a coffee break)
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)