MAGIC-5 ad Alexandria (Suzanne Mubarak Centre) P. Cerello (INFN Torino)

Transcription

1 MAGIC-5 ad Alexandria (Suzanne Mubarak Centre) P. Cerello (INFN Torino)

2 LNF, May 22 nd,

3 The Suzanne Mubarak Regional Centre for Women s Health and Development, Alexandria, Egypt LNF, May 22 nd, 2007 cerello@to.infn.it 3

4 Suzanne Mubarak Centre Mission To promote knowledge and services in the field of women s health in Egypt, the Arab World, the Middle East and Africa Inauguration on Mar, 21 st, 2007

5 Vision 1. Training doctors, nurses and health administrators 2. Conducting research 3. Running community service projects 4. Maintaining an information centre 5. Organising and participating in workshops, seminars and medical conferences 6. Conducting women s development activities 7. Running model clinics

6 The teleconference room LNF, May 22 nd,

7 Model clinics 1. Prenatal diagnosis of congenital disease 2. High risk pregnancy clinic 3. Well woman s clinic 4. Aesthetic dermatology clinic 5. Diet control clinic 6. Uro-gynaecology clinic 7. Infertility/repeated miscarriages clinic

8 Model clinics (cont ) 8. Internal medicine and endocrine clinic 9. Breast and surgery clinic 10. Oncology clinic 11. Neonatal screening clinic 12. Diabates in pregnancy clinic 13. Dental clinic 14. Genetic/premarital counseling clinic

9 The well woman s clinic 1. Pap smear 2. Ultrasound 3. Mammography 4. DEXA 5. Lipid profile

10 The Analysis Station MASSES MICROCALCIFICATIONS Massive Lesion Microcalcifications Hospitals Lecce Ovada (Al) Torino (Valdese) Alexandria INFN Bari Genova Lecce Palermo Pisa Sassari Torino LNF, May 22 nd,

11 the Analysis Station in Alexandria first contact with dr. Hassan Sallam (Director of the Suzanne Mubarak Centre for Women s Health and Development) in the summer of 2006 by S. Bertolucci and B. Gallavotti, during the installation of Microscopi della Fisica in Alexandria the MAGIC-5 Mammogram Analysis Station was installed and configured in Mar2007 it will work with an analog Mammograph donated by the UN PC Dual Core 600 GB disk 2 GB RAM Photo Scanner Monitor 32 Philips Total cost: 3kE LNF, May 22 nd, 2007 cerello@to.infn.it 11

12 the Analysis Station in Alexandria data taking will start soon (mammograph not available in March) upgrade in May so as to start its use as Computer Assisted Diagnosis tool INFN will provide remote support and upgrades to the CAD Station the radiologist team coordinated by dr. E. Zanon (Senologia at Ospedale Valdese, Ospedale Cottolengo - Torino -, Regional Screening in Mondovi and Ceva, Examina Medical Centre - Torino -) is available to assist the SMC Radiologist Team in teleradiology mode (if the network bandwidth will allow it) LNF, May 22 nd, 2007 cerello@to.infn.it 12

13 The Analysis Station Load Exam Images from scanner or dicomdir Insert Patient and Exam related metadata Insert Diagnosis Store Exam (1 exam = 1 directory) Image data in DICOM format (1 file/image) Metadata in ROOT format (exam.root) Image Manipulation: zoom, contrast, luminosity, negative image Image Analysis: Average Breast Density (i.e., luminosity) (global &/or local) Pixel intensity distribution Masses Computer Assisted Detection Microcalcifications Computer Assisted Detection LNF, May 22nd, 2007 cerello@to.infn.it 13

14 The CALMA DATABASE N tot =3369 N paz =967 LNF, May 22 nd, 2007 cerello@to.infn.it 14

15 Masses Analysis Algorithm: results Az = ± FP/image Sensitivity 66 % 70% 80 % Published on Medical Physics Vol. 33, No. 8, Aug 2006, pp LNF, May 22 nd, 2007 cerello@to.infn.it 15

16 Microcalcifications Analysis Algorithm 1 - Preprocessing Sample #patients #images Sensitivity FP/image CALMA DB (477/494) 18.3 MIAS DB (15/15) 20.0 DDSM DB: ongoing 2 - Classification FP rejection can be improved The NN does not converge as well as we would like: - the clustering after the preprocessing is being improved LNF, May 22 nd, 2007 cerello@to.infn.it 16

17 Density Comparison Code for the scale normalisation was developed based on the overlap of the area outside the breast Breast range starts here Breast range starts here Outside the breast (1/3) Inside the breast (2/3) Density before and after treatment is constant (within 1%) on right and left breast - 20 more exams coming soon LNF, May 22 nd, 2007 cerello@to.infn.it 17

18 Where are we - CAD? Masses ROI hunter could be improved Microcalcifications Excellent performance of preprocessing Classification (Clustering) can be improved Density comparison (on digital mammograms) Consistent results: density constant within 1% on right and left breasts (CC view) before and after hormonal treatment (statistics to be improved) Digital Mammograms Some available, but a large DB is required to test the algorithms on images with different features (resolution, dynamic range, etc ) LNF, May 22 nd, 2007 cerello@to.infn.it 18

19 What for the future? Transition to Digital devices Need a Digital Database (better quality, better performance expected, but tuning required) Shall we do some more work? Which partner(s)? BRACCO Imaging ASL (Screening Programs) What is our task? i.e., how far shall we go? What human and financial resources? LNF, May 22 nd, 2007 cerello@to.infn.it 19

20 Regione Umbria (Screening) Accordo con ASL Perugia per realizzazione DB di immagini digitali refertate 104 esami acquisiti, 40 refertati (161 immagini) 34 microcalcificazioni 48 lesioni massive Primo test preliminare (algoritmo as it is ): ~75% sensibility su microcalcificazioni, FP ~ 16 prima della classificazione Il preprocessore mostra risultati compatibili con le immagini digitalizzate LNF, May 22 nd, 2007 cerello@to.infn.it 20

21 Regione Puglia (Screening) Possibile Collaborazione per programma di Screening Mammografico LNF, May 22 nd,

22 CPO* Piemonte & INFN, UniTo * Centro Prevenzione Oncologica Regional Mammographic Screening exams/year (75% of women in the age range): about 6 TB/y 9 Departments, 33 centres + 6 mobile centres, 54 mammographs Proposal for a full upgrade to Digital Mammography Deployment and use of Grid Services for the analysis of distributed data Simple analysis on a large sample (e.g., average intensity distribution) CAD algorithms on the full data sample ---> Training, testing ---> Validation If the Digital upgrade will be funded, a proposal will be submitted in the framework of the Legge Regionale sulla Ricerca LNF, May 22 nd, 2007 cerello@to.infn.it 22

23 Altri contatti Latina (ASL) Richiesta di installazione ed uso della stazione Camerino (Universita ) Richiesta di uso del Database CALMA Bassano del Grappa (ASL) Ricerca di uno strumento di CAD per Screening su dati distribuiti LNF, May 22 nd, 2007 cerello@to.infn.it 23

24 Why Grid Services? Intrinsically distributed Database many sources Access all the images with minimum data transfer Network connections / Data ownership The GRID philosophy in mammographic CAD Use Cases Large Scale Screening - batch Analysis on demand - interactive Example: Screening in Italy 4 mammograms/exam 6.7 Mpeople, 1 exam/2y 3.35 Mexams/year about 130 TB/year 1 PB/year on the European scale Huge amount of distributed data LNF, May 22 nd, 2007 cerello@to.infn.it 24

25 Grid Implementation Choices - Analyse Data Where they are stored (privacy, ownership) - Many small sites ( = hospitals) Grid Services: AliEn User Management Data Management (Catalogue, Storage) Job Management Interactivity: PROOF GSI Authentication Dataset and Selector Class with user analysis code Drawback: data MUST be stored in a ROOT Tree LNF, May 22 nd, 2007 cerello@to.infn.it 25

26 Deployment configuration Node VO Client magic5.to.infn.it Node VO Client Node VO Client Node VO Grid Server Central Services System Configuration Users Database Data Catalogue PROOF Master Node VO Client VO Client File Transfer Service Clients installed: Bari, Genova, Lecce, Palermo, Pisa, Torino Site Services Compute Element Storage Element File Transfer Service PROOFd (now xrootd) GPCALMA (application) LNF, May 22 nd,

27 Start PROOF Cluster PROOF Cluster End ofexam Task Working PROOF Cluster The MAGIC-5 Query on Patient Data Register a new GSI Authentication Required Login: User Authentication Display (or Save) Results Ongoing Analysis Analysis Station GUI to Grid Services Find Retrieve) Exams in the(& Data Catalogue Send CALMASelector.C code for distributed interactive execution using the CINT Interpreter The MAGIC-5 Mammogram Analysis Station LNF, May 22, 2007 cerello@to.infn.it nd 27

28 Lung CT Analysis How about ANTS for the segmentation as well? n1 Problem: the large number of false positives Strategy: many approaches with 100% sensitivity (S) in logical AND n2 Segmentation: find the lung volume Pleural 42 scans with 102 nodules: 80% S with 35 FP/scan Dot-Enhancement (D-E) 24 scans with 45 n1 nodules: 86.7% S with 5 FP/scan Image Likelihood Region Growing + Linear Filter (Area, Sphericity, Intensity) Matrix Matrix n3 19 scans with 26 (15n1 + 11n2) nodules, 96% S with about 1.7 List of FP/scan Virtual Ants Peaks (ROIs) 19 scans, with 16 n1/n2 nodules: 96%, with about 4.2 FP/scan on D-E output > 16 FP/scan before classification!!!! LNF, May 22nd, 2007 cerello@to.infn.it 28

29 Lung CT Drafts Pleural nodules Ready for submission Internal Nodules Dot-enhancement ready for submission Common Approach Region-Growing: second internal review, to be sent to Medical Physics ANTS: model implementation: to be submitted to Pattern Recognition ANTS on lung CT: ongoing test & draft being prepared LNF, May 22 nd,

30 Neuroimages Activity being started (Bari, Genova, Lecce, Napoli, Torino) coordination to be discussed at next Collaboration Meeting (Napoli, June) The problem is less defined with respect to the analysis of mammograms and lung CTs Correlation markers between image properties and the Alzheimer s disease are UNKNOWN If any is found, the job is done LNF, May 22 nd, 2007 cerello@to.infn.it 30

31 Conclusioni MAGIC-5 ha interesse a e intenzione di cercare di far utilizzare il piu possibile la stazione mammografica La scelta su come procedere e anche politica La scala di applicazione e ~ Regionale le risorse necessarie sono rilevanti BRACCO Imaging e/o altre aziende? Open Source? LNF, May 22 nd, 2007 cerello@to.infn.it 31