an open-source, matlab-based annotation tool for virtual...
TRANSCRIPT
![Page 1: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/1.jpg)
© 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
![Page 2: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/2.jpg)
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
![Page 3: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/3.jpg)
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
![Page 4: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/4.jpg)
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
![Page 5: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/5.jpg)
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
![Page 6: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/6.jpg)
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
![Page 7: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/7.jpg)
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
![Page 8: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/8.jpg)
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
![Page 9: An open-source, MATLAB-based annotation tool for virtual ...mitel.dimi.uniud.it/tp2012/presentations/A6-Turkki.pdf · An open-source, MATLAB-based annotation tool for virtual slides](https://reader033.vdocuments.site/reader033/viewer/2022050306/5f6e88a12ebff23d4828e46d/html5/thumbnails/9.jpg)
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!