Training school in the use of Open Source Image Analysis Software in Pathology
24-26th June, 2009. Nottingham, UK

SCIENTIFIC PROGRAMME
 

Day 1. 24th JUNE

09:00 – 09:30 Introduction – the role of image analysis in Pathology (covering: image analysis as diagnostic aids / telepathology / image analysis in research etc.) – Marcial García Rojo
 

09:30 – 10:15 What is a digital image? (covering: pixels, formats such as jpg/bmp/tiff etc, brightfield images – rgb/cmyk/cielab/binary transformation, multispectral images) – Branimir Reljin

10:15 – 10:45 Tea / Coffee
 

10:45 – 11:30 Methods of image capture and viewing (covering: digital photography, the different slide scanners, commercial software sold with scanners, use of ImageJ to view scanned images). - Marcial García Rojo
 

11:30 – 12:15 Basic use of imageJ (covering: the basic functions/tools of the program, measuring size and area, counting particles manually etc) - Vincenzo Della Mea
Slides first part  

12:15 - 12:30 Loading ImageJ onto laptops (including plug-ins)
 

12:30 – 13:30 Lunch
 

13:30 – 14:00 Worked examples with ImageJ (Led by Vincenzo Della Mea)
second part slides, third, and fourth file. The ImageJ web site is here: http://rsb.info.nih.gov/ij/ .  

14:00 – 15:30 Practical session of easy image analysis problems (Led by Vincenzo Della Mea)
 

15:30 – 16:00 Tea / coffee
 

16:00 – 17:00 Going through practical examples (Led by Vincenzo Della Mea)
 

Day 2. 25th JUNE

09:00 – 09:45 Image fragmentation (covering: identifying and marking ROIs, applying masks to sequential images)  – Qiu Guoping
 

09:45 – 10:15 Worked examples with ImageJ (Led by Paulette Herlin)
 

10:15 – 10:45 Tea / coffee
 

10:45 – 12:15 Practical session of image analysis problems (Led by Paulette Herlin)
 

12:15 – 12:45 Going through practical examples  (Led by Paulette Herlin)
 

12:45 – 13:45 Lunch
 

13:45 – 14:15 Further image fragmentation (covering: segmentation, binary transformation, particle counting, thresholding) – Gabriel Landini
 

14:15 – 14:45 Worked examples with ImageJ (Led by Gabriel Landini)
 

14:45 – 15:30 Practical session of image analysis problems (Led by Gabriel Landini)
 

15:30 – 16:00 Tea / Coffee
 

16:00 – 16:30 Practical session of image analysis problems (Led by Gabriel Landini)
 

16:30 – 17:00 Going through practical examples (Led by Gabriel Landini)


 

Day 3. 26th JUNE

09:00 – 09:45 More fragmentation analysis (texture analysis, k-means clustering)  – Gabriel Landini
 

09:45 – 10:30 Immunohistochemistry (covering: nuclear / cytoplasmic / membranous staining, segmentation and thresholding, viewing through RGB / Cielab., TMA databasing) - Marcial García Rojo
 

10:30 – 11:30 Practical session of image analysis problems (Led by Marcial García Rojo) and Coffee
 

11:30 – 12:00 Going through practical examples (Led by Marcial García Rojo)
 

12:30 – 13:30 Presentation by Slidepath
(i) SlidePath image analysis algorithms,
(ii) integrating Image J into slidepath,
(iii) (iii) Databasing and high-throughput analysis

13:30 – 14:30 Lunch and finish
 

Organized by: COST Action IC0604 - EURO-TELEPATH and the University of Nottingham.
 

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