Workshop on Quantitative Microscopy:

Digital imaging of whole slides, image analysis, and stereology

September 8 th – 12 th, 2009

TENTATIVE COURSE SCHEDULE (Subject to change)

Participants please bring : A laptop, calculator with square root function, a pair of scissors, a sharp kitchen paring knife and a metric ruler. All other course materials will be supplied, including instructional materials.

REGISTRATION AND RECEPTION -

September, 7th 2009

12:00 to 17:00 Registration

18.30 - Get-Together-Dinner

THEORETICAL AND PRACTICAL STEREOLOGY

TUESDAY - September, 8 th 2009

10.00 - 10.45 Lecture: Definition of probes, sampling and basic statistics HG/DH

10.45 - 11.30 Lecture: Volume estimation, Cavalieri principle DH

11.30 - 12.30 Exercise: Volume estimation DH

12.30 - 14.00 Lunch

14.00 - 14.45 Lecture: The fractionator principle (systematic sampling) HG/JN

14.45 - 15.45 Exercise: The fractionator JN

15.45 - 16.15 Coffee

16.15 - 17.00 Lecture: The disector, counting and sampling in 3D JN

17.00 - 18.00 Exercise: Number estimation JN

18.30 - Dinner

WEDNESDAY - September, 9 th 2009

09.00 - 09.45 Lecture: Length and Surface, IUR JN

09.45 - 10.45 Exercise: Length estimation DH

10.45 - 11.15 Coffee

11.15 - 12.00 Lecture: Estimation via ratios, multilevel sampling design DH

12.00 - 13.00 Lecture: How many animals, blocks, sections? HG/JN

13.00 - 14.00 Lunch

14.00 - 15.00 Demonstration: Computer-assisted stereology LL 15.00 - 15.15 Coffee

15.15 - 16.00 Lecture: More disector sampling, including connectivity JN

16.00 - 17.00 Exercise: Connectivity DH/JN

19.00 - Dinner

THURSDAY - September, 10 th 2009

09.00 - 09.30 Lecture: Vertical sections JN

09.30 - 11.00 Exercise: Surface from vertical sections – bananametry JN

11.00 - 11.15 Coffee

11.15 - 12.00 Exercise: Length from vertical projection – roots JN

12.00 - 13.00 Lunch

13.00 - 13.45 Lecture : Tissue deformation, slicing, sectioning, tools and gadgets JN

13.45 - 14.30 Lecture: Sampling and Sizing of particles HG/JN

14.30 - 15.00 Coffee: Stereology evaluation JN

15.00 - 16.00 Exercise: The nucleator DH

16.00 - 16.45 Exercise: Point sampled intercept DH

IMAGE ANALYSIS, DIGITAL IMAGING, AND PRACTICAL EXERCISES

FRIDAY - September, 11 th 2009

9.00 - 9.45 Lecture : Basic overview of microscopy and digital imaging OAI

9.45 - 10.30 Demonstration: Whole slide digital imaging /virtual microscopy OAI

10.30 - 10.45 Coffee

10.45 - 11.30 Workshop: Participant applications: Hands-on scanning and microscopy. Generation of image material for afternoon exercises. OAI

11:30- 12.00 Lecture: Basics of image analysis and segmentation LAP

12.00 - 13.00 Lunch

13:00 - 14.00 Lecture: Advanced image analysis: How to include structural and contextual information. Demonstration of VisioMorph. LAP

14.00 - 15.00 Exercise: Design of image analysis protocols, part 1 LAP

15.00 - 15.15 Coffee

15:15 - 16.45 Exercise: Design of image analysis protocols, part 2

(Participants images) LAP

SATURDAY - September, 12 th 2009

09.00 - 10.30 Lecture: Introduction to new CAST LL

10.30 - 10.45 Coffee

10.45 - 11.30 Exercise : Analysis of alveolar surface area LL

11.30 - 12.15 Exercise: Analysis of alveolar number LL

12.15 - 13.15 Lunch

13.15 - 15.00 Workshop: Participant applications: Discussion of case examples All

15.00 – 15:15 Coffee

15.15 – 16.00 Lecture: New tools in stereology: The AutoDisector and Proportionator. LL

16.00 - 16.45 Round up and discussion All