Bisque: A Platform for Bioimage Analysis and Management -
Supplementary material
Kristian Kvilekval, Dmitry Fedorov, Boguslaw Obara, Ambuj Singh and B.S. Manjunath
December 11, 2009
Contents
1 Web interface screen-shots 3
2 Flexible metadata XML format description 7
2.1 Use examples of flexible meta-data XML ...................................... 7
2.1.1 Microtubule tracking ............................................. 7
2.1.2 Annotation used by Greenpeace researchers studying the effects of Deep Sea Trolling ......... 9
2.1.3 Annotation of Arabidopsis Thaliana with automatically detected nuclei ................ 11
2.1.4 Retinal image annotation .......................................... 12
2.1.5 An example of an embedded metadata reported by ImageServer .................... 13
3 Bisque component details 14
3.1 Data Server ...................................................... 14
3.1.1 Search query examples ............................................ 14
3.2 Image Server ..................................................... 15
3.3 Additional Services .................................................. 16
3.4 Modules for Retinal studies ............................................. 17
3.5 Modules for Microtubule studies .......................................... 17
3.6 Modules for Benchmarking studies ......................................... 17
3.7 Using Curl to interact with Bisque ......................................... 18
4 Details about web-applications presented in case studies 19
4.1 3D Nuclei detection ................................................. 19
4.2 Microtubule tracking ................................................. 19
5 External Tools 22
5.1 DigitalNotebook ................................................... 22
5.2 BioView ........................................................ 24
5.3 BioView3D ...................................................... 26
6 Deployment details 28
6.1 Bisque system ..................................................... 28
6.2 Analysis benchmarking ................................................ 28
7 Implementation details 29
7.1 Developer Resources ................................................. 29
7.2 Module Definitions .................................................. 29
7.3 Bisque API ...................................................... 30
7.4 Example Matlab module ............................................... 30
8 Performance evaluation and usage statistics 31
8.1 Performance evaluation ............................................... 31
8.1.1 Performance of thumbnail fetching ..................................... 31
8.1.2 Performance of tag modifications ...................................... 31
8.2 Usage statistics .................................................... 32
1