an open-source, matlab-based annotation tool for virtual...
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© 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!