Image Classification Optimization of High Resolution Tissue Images
Generic image classification methods are not performing well on tissue images. Such software solutions are producing high number of false negative and positive results, which prevents their clinical usage. We have created the MorphCeck high resolution tissue image processing framework, which enables us to collect morphological and morphometrical parameter values of the examined tissues. Size of such tissue images can easily reach the order of 100 MB–1 GB. Therefore, the image processing speed and effectiveness is an important factor. Our main goal is to accurately evaluate high resolution H-E (hematoxilin-eozin) stained colon tissue sample images, and based on the parameters classify the images into differentiated sets according to the structure and the surface manifestation of the tissues. We have interfaced our MorphCheck tissue image measurement software framework with the WND-CHARM general purpose image classifier and tried to classify high resolution tissue images with this combined software solution. The classification is by default initiated with a large training set and three main classes (healthy, adenoma, carcinoma), however the new image classification process’ wall-clock time was intolerably high on single core PC. The processing time is depending on the size/resolution of the image and the size of the training set. Due to the tissue specific image parameters the classification effectiveness was promising. So we have started a development process to decrease the processing time and further increase the accuracy of the classification. We have developed a workflow based parallel version of the MorphCheck and WND-CHARM classifier software. In collaboration with the MTA SZTAKI Application Porting Centre the WND-CHARM has been ported to some distributed computing infrastructure (DCI). The paper introduces the steps that were taken to optimize WND-CHARM applications running faster using DCIs and some performance results of the tissue image classification process.
KeywordsApplication porting Medical image processing workflow HP-SEE gUSE Scalability MorphCheck WND-CHARM
The authors would like to thank two projects for their financial support. This work was supported by the HP-SEE (High-Performance Computing Infrastructure for South East Europe’s Research Communities, under contract no. RI-261499) project and by the 3DHistech08 project, the Hungarian National Technology Programme, A1, Life sciences, the “Development of integrated virtual microscopy technologies and reagents for diagnosing, therapeutical prediction and preventive screening of colon cancer”. Authors would like to thank Semmelweis University and Major & Co. to provide us annotated tissue samples for processing and classification. Authors would like to thank for the technical support of the WND-CHARM developer team as well.
- 1.3DHistech. http://www.3DHistech.com. Accessed 09 Feb 2013
- 2.Aperio. http://www.aperio.com. Accessed 09 Jan 2013
- 3.Definiens. http://www.definiens.com. Accessed 09 Jan 2013
- 4.Visiopharm. http://www.visiopharm.com. Accessed 15 Feb 2013
- 5.Kacsuk, P., Farkas, Z., Sipos, G., Hermann, G., Kiss, T.: Supporting workflow-level PS applications by the P-GRADE grid portal. In: Towards Next Generation Grids Proceedings of the CoreGRID Symposium (2007)Google Scholar
- 7.Szénási, S., Vámossy, Z., Kozlovszky, M.: Evaluation and comparison of cell nuclei detection algorithms. In: 16th International Conference on Intelligent Engineering Systems (INES), Lisbon, July 2012, pp. 469–475 (2012). ISBN: 978-1-4673-2694-0Google Scholar
- 8.MorphCheck. http://biotechweb.nik.uni-obuda.hu/web/en/research/projects/3dhist08/morphcheck2. Accessed 09 Feb 2013
- 9.http://www.grc.nia.nih.gov/branches/lg/iicbu/iicbu.htm. Accessed 09 Feb 2013
- 10.HP-SEE. http://www.hp-see.eu. Accessed 09 Feb 2013
- 11.Libtiff. http://www.libtiff.org. Accessed 09 Feb 2013
- 12.FFTW. http://www.fftw.org/download.html. Accessed 09 Feb 2013