title: The application of JPEG2000 in virtual microscopy.
abstract: Virtual microscopy (i.e., the viewing of entire microscope specimens on a computer display) is becoming widely applied in microscopy teaching and clinical laboratory medicine. Despite rapidly increasing use, virtual microscopy currently lacks of a universally accepted image format. A promising candidate is JPEG2000, which has potential advantages for handling gigabyte-sized virtual slides. To date, no JPEG2000-based software has been specifically suited for virtual microscopy. To study the utility of JPEG2000 in virtual microscopy, we first optimized JPEG2000 code-stream parameters for virtual slide viewing (i.e., fast navigation, zooming, and use of an overview window). Compression using ratios 25:1-30:1 with the irreversible wavelet filter were found to provide the best compromise between file size and image quality. Optimal code-stream parameters also consisted of 10 wavelet decomposition levels, progression order Resolution-Position-Component-Layer (RPCL), a precinct size of 128 x 128, and code-block size of 64 x 64. Tiling and the use of multiple quality layers were deemed unnecessary. A compression application (JVScomp) was developed for creating optimally parameterized JPEG2000 virtual slides. A viewing application (JVSview) was developed specifically for virtual microscopy, offering all of the basic viewing functions. JVSview also supports viewing of focus stacks, embedding of textual descriptions, and defining regions of interest as metadata. Combined with our server application (JVSserv), virtual slides can be viewed over networks by employing the JPEG2000 Interactive Protocol (JPIP). The software can be tested using virtual slide examples located on our public JPIP server ( http://jvsmicroscope.uta.fi/ ). The software package is freely downloadable and usable for noncommercial purposes.
authors.affiliation: Institute of Medical Technology, Tampere University Hospital, University of Tampere, Tampere, Finland. vilppu.tuominen@iki.fi
authors.forename: Vilppu J
authors.initials: VJ
authors.lastname: Tuominen
authors.forename: Jorma
authors.initials: J
authors.lastname: Isola
mesh_terms: D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008853:Microscopy / Q000379:methods* / Q000639:trends; D011381:Programming Languages; D012815:Signal Processing, Computer-Assisted; D012984:Software / Q000639:trends; D014584:User-Computer Interface