© FIMM - Institiute for Molecular Medicine Finland www.fimm.fi

08.06.2012

An open-source, MATLAB-based annotation tool for virtual slides

Riku Turkki – TP2012

FIMM – Institute for Molecular Medicine Finland

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 2

Definitions & aims

The tool

Other applications

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 3

Virtual slides

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 4

Virtual microscopy

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 5

An open-source, MATLAB-based annotation tool for virtual slides.

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 6

Image analysis

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 7

Image analysis

development

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 8

Definitions & aims

The tool

Other applications

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 9

An open-source, MATLAB-based annotation tool for virtual slides.

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 10

The annotation tool A B C

Caseid = c1 URL = Height = Width = Number of tiles Date Annotations Seen tiles . . . EOF

Tile #185 [9,11] Location : label [302 , 13]: 1 [1024, 21]: 1 [300 , 512]: 1 [792 , 281]: 2 [1102, 152]: 1 . . . EOF

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 11

The annotation tool

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 12

The annotation tool

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 13

.ecw + .jp2

ImageX

.jp2

JPIP

The annotation tool

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 14

.ecw + .jp2

ImageX

.jp2

JPIP

The annotation tool

www.fimm.fi Presentation name or name of the guest dd.mm.yyyy 15

The annotation tool

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 16

Definitions & aims

The tool

Other applications

www.fimm.fi An open-source, MATLAB-based annotation tool for virtual slides. 08.06.2012 17

Possible applications

› Quality control ! Number of annotations ! Distance between annotations

› Education ! Homework ! Exams

› Metadata for virtual slides ! Share your annotations

Thank You!