The Tiling Suite
A collection of program to prepare, create and visualize deep focus images
Welcome
Tiling Suite programs are an attempt to answer some of the many problems connected with digital cytology. Micro focusing is essential in cytology because the cells are dispersed and lie on different levels in the mounting medium. The aim of Tiling Suite programs is to create a digital zoomable image where all the cells lie on a single level and are perfectly focused without the micro focusing need, so as to provide a platform for e-learning, testing and training.
The process starts from a multi z-stack level virtual slide scanned with a Hamamatsu™ scanner for digital pathology. Using open source software (NDPITools) all the levels of the virtual slide are read and decomposed in thousands (sometimes hundreds of thousands) small images called “tiles”. The best tiles are selected and used to compose a new image where all the cells are in focus. The algorithm performing this kind of deep focusing is original and is the base of the MicroTiling, ServerTiling and ServerTiling Interface programs in the Tiling Suite.
I have to thanks some people.
- Jeremy Cooke, Senior Analyst Programmer at Hamamatsu Photonics™, for his patience and courtesy explaining me how to manage .ndpi files.
- Christophe Deroulers, author of NDPITools. Without his work mine would not be possible.
- A special thanks to all the colleagues and friends who worked and are still working in the Eurocytology Project. Without their sympathy and support and (especially) without Eurocytology, Tiling Suite would never have been born.
Tiling Suite is free software. You are free to use and distribute it along with this introduction and manual. You are not allowed to sell it. If you are using it for Academic purposes please cite the author.
Arrigo Capitanio, Pathologist
Department of Pathology
Linköping University Hospital
Linköping, 25th June 2017
Tiling Suite is the result of some years of work and research on digital imaging. It is not perfect and certainly it is not the final solution. It is simply my passionate contribution tackling the problem of digital cytology.
Disclaimer.
All the software included in Tiling Suite is free software. Everybody can use and distribute it along with this introduction and manual. The software is intended for academic, educational and scientific purposes.
NOT FOR DIAGNOSTIC USE.
If you use this software is your responsibility to test it and verify if it suits for your purposes. No warranty is given and no liability of the author for any damage arising from the use of this software.