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

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

Virtual slides

Virtual microscopy

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

Image analysis

development

Definitions & aims

The tool

Other applications

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

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

The annotation tool

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ImageX

The annotation tool

.ecw + .jp2

ImageX

The annotation tool

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

The annotation tool

Definitions & aims

The tool

Other applications

Possible applications

› Quality control ! Number of annotations ! Distance between annotations

› Education ! Homework ! Exams

› Metadata for virtual slides ! Share your annotations

Thank You!

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

Documents

NCBI’s Genome Annotation: Overview Incremental processing Re-annotation ( batch ) Post-annotation review Case studies NOTE: limiting discussion to annotation

Annotation! · Annotation! Learn it! Live it! Love it! Become familiar with annotation methods -Develop specific reading strategies -Understand how to use annotation to organize and

LaTeX in Matlab - Auburn Universityreevesj/Classes/ELEC6970-latex/matlab/Matlab… · Figure Annotation M-File Publishing Matrices LATEX in Matlab Aaron Biddings Electrical and Computer

Pathema Burkholderia Annotation Jamboree: Introduction to Annotation Jamboree

Annotation consistency using annotation intersections

Genome Annotation - University of California, Santa Cruz · Genome Annotation Repeat Annotation For Gene Annotation 1 RepeatMasker -pa xx -gccalc -nolow -species aves genome.fasta

AATOS – a Conﬁgurable Tool for Automatic Annotation · annotation tools where the annotation process can be performed as swiftly as possible. The entrance barrier to annotation

Annotation systems

Spread annotation

DRAFT - Version 1/27/2014 - Annotation Studio · Type your annotation into the Annotation Editor. !!!!! 3.5 Tags and privacy options! Below the annotation ﬁeld in the Annotation

Utility data annotation with Amazon Mechanical Turkvision.cs.uiuc.edu/annotation/papers/cvpr08_annotation_submission.pdfUtility data annotation with Amazon Mechanical Turk Anonymous

The Image- and Data Quality Ontology for scientiﬁc data ...mitel.dimi.uniud.it/tp2012/presentations/B4-Schrader.pdf · Delphi-Method - Discusion and determination of quality criteria

Newspaper Annotation

DIAGNOSTIC REPRODUCIBILITY ON A DIGITAL SLIDE …mitel.dimi.uniud.it/tp2012/presentations/C4-Lega.pdf · DIGITAL SLIDE EVALUATION SYSTEM IN CYTOLOGICAL AND HISTOLOGICAL ONCOLOGIC

HRVTool – an Open-Source Matlab Toolbox for Analyzing Heart Rate Variability · and manual adjustments of beat locations are possible and the corresponding annotation ﬁle can

Review Free EGASP: the human ENCODE Genome Annotation ...repository.cshl.edu/25307/1/...Genome-Annotation...Automatic genome annotation methods To date, accurate automatic annotation

Package ‘annotationTools’ - bioconductor.riken.jp fileThe annotation is returned as elements of list ’annotation’. If a single annotation is given for a If a single annotation

Annotation and Evaluation - GATE · University of Sheffield, NLP Topics covered • Defining annotation guidelines • Manual annotation using the GATE GUI • Annotation schemas

Treebank annotation

Protein Functional Annotation · Annotation! Michelle Giglio! Protein Functional Annotation! •!Experimental knowledge of function! •!Literature curation! •!Perform experiment!