IBM Research Report. Semantic Model Vector Training Data for ImageCLEF2013
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1 RC25474 (WAT ) June 6, 2014 Computer Science IBM Research Report Semantic Model Vector Training Data for ImageCLEF2013 Noel Codella, Michele Merler IBM Research Division Thomas J. Watson Research Center P.O. Box 218 Yorktown Heights, NY USA Research Division Almaden Austin Beijing Cambridge Dublin - Haifa India Melbourne - T.J. Watson Tokyo - Zurich
2 IBM Research Report: Semantic Model Vector Training Data for ImageCLEF2013 Noel Codella 1 and Michele Merler 1 IBM T.J. Watson Research Center, 1101 Kitchawan Rd., Yorktown Heights, NY Abstract. In this research report, we describe the dataset used to train the semantic model vector employed for the ImageCLEF 2013 medical modality visual classification task. 1 Introduction The medical semantic model vector used for the ImageCLEF 2013 medical modality recognition task [1, 2] is trained from about 26,000 images collected from multiple sources, organized into a hierarchical taxonomy structure of 120 categories of various radiological categories. The images used to train our semantic model vector were acquired from web crawled data, the Image Retrieval in Medical Applications (IRMA) 2009 dataset [3], The Cancer Imaging Archives (TCIA) [4, 5], Cornell University SIMBA CT dataset [6], and the Japanese Society of Radiological Technology (JSRT) [7]. Web crawl was performed using the Microsoft Bing search engine, with queries as the semantic concept label (abbreviations expanded). The top 500 results were saved, and cleaned by a human labeler. Each dimension in the model vector refers to a subcategory over 7 modality domains of CT, X-Ray, ECG, MRI, PET, Ultrasound, and Slide Microscopy. The rest of the dimensions represent subcategories covering body regions (such as chest, arm, leg, head, brain, neck, etc.), views (such as anterio-posterior, coronal, saggital), and disease states (such as pneumothorax) under each modality. 2 Categories & Number of Examples This section gives a full accounting of the name of each semantic classifier in the semantic model vector, along with the number of positive examples used for training (in parentheses). CT (10055) CT BRAIN (131) CT CHEST (9924) CT CHEST LUNGCANCER (92) CT CHEST NORMAL (9690) CT CHEST PNEUMOTHORAX (142) DX (12995) DX APPENDAGE (4650)
3 2 DX APPENDAGE ARM (2422) DX APPENDAGE ARM ELBOW (371) DX APPENDAGE ARM ELBOW AP (151) DX APPENDAGE ARM ELBOW LAT (220) DX APPENDAGE ARM FOREARM (157) DX APPENDAGE ARM FOREARM AP (75) DX APPENDAGE ARM FOREARM LAT (82) DX APPENDAGE ARM HAND (1188) DX APPENDAGE ARM HAND FINGER (158) DX APPENDAGE ARM HAND WHOLE (798) DX APPENDAGE ARM HAND WHOLE AP (688) DX APPENDAGE ARM HAND WHOLE OBL (110) DX APPENDAGE ARM HAND WRIST (232) DX APPENDAGE ARM HAND WRIST AP (114) DX APPENDAGE ARM HAND WRIST LAT (118) DX APPENDAGE ARM SHOULDER 32 (632) DX APPENDAGE ARM UPPER (74) DX APPENDAGE LEG (2228) DX APPENDAGE LEG ANKLE (345) DX APPENDAGE LEG ANKLE AP (177) DX APPENDAGE LEG ANKLE LAT (168) DX APPENDAGE LEG FOOT (672) DX APPENDAGE LEG FOOT AP (408) DX APPENDAGE LEG FOOT LATERAL (122) DX APPENDAGE LEG FOOT OBLIQUE (142) DX APPENDAGE LEG KNEE (829) DX APPENDAGE LEG KNEE PATELLA (103) DX APPENDAGE LEG KNEE WHOLE (726) DX APPENDAGE LEG KNEE WHOLE AP (442) DX APPENDAGE LEG KNEE WHOLE LAT (284) DX APPENDAGE LEG LOWER (191) DX APPENDAGE LEG LOWER AP (125) DX APPENDAGE LEG LOWER LAT (66) DX APPENDAGE LEG UPPER (191) DX APPENDAGE LEG UPPER AP (133) DX APPENDAGE LEG UPPER LAT (58) DX CRANIUM (1070) DX CRANIUM NOSE (314) DX CRANIUM NOSE LAT (50) DX CRANIUM NOSE OCCIPITOFRONTAL (264) DX CRANIUM WHOLE (756) DX CRANIUM WHOLE AP (358) DX CRANIUM WHOLE FRONTOCCIPITAL (38) DX CRANIUM WHOLE LAT (360) DX HIP JOINT AP ARTIFICIAL (84)
4 DX HIP JOINT AP NATURAL (127) DX HIP JOINT LAT ARTIFICIAL (21) DX HIP JOINT LAT NATURAL (53) DX TORSO (7275) DX TORSO ABDOMEN (379) DX TORSO ABDOMEN AP (204) DX TORSO ABDOMEN BARIUMSWALLOW (143) DX TORSO ABDOMEN UPPER (32) DX TORSO BREAST (262) DX TORSO BREAST LEFT (128) DX TORSO BREAST LEFT AXIAL (63) DX TORSO BREAST LEFT OBL (65) DX TORSO BREAST RIGHT (134) DX TORSO BREAST RIGHT AXIAL (65) DX TORSO BREAST RIGHT OBL (69) DX TORSO CHEST (4583) DX TORSO CHEST FULL (4583) DX TORSO CHEST FULL AP (3728) DX TORSO CHEST FULL AP LUNGCANCER (183) DX TORSO CHEST FULL AP NORMAL (302) DX TORSO CHEST FULL AP PNEUMONIA (204) DX TORSO CHEST FULL AP PNEUMOTHORAX (164) DX TORSO CHEST FULL AP UNKNOWN (2875) DX TORSO CHEST FULL LAT (855) DX TORSO CHEST FULL LAT LUNGCANCER (1) DX TORSO CHEST FULL LAT NORMAL (18) DX TORSO CHEST FULL LAT UNKNOWN (836) DX TORSO HIP (643) DX TORSO HIP JOINT (285) DX TORSO HIP JOINT AP (211) DX TORSO HIP JOINT LAT (74) DX TORSO HIP PELVIS (358) DX TORSO HIP PELVIS ARTIFICIAL (74) DX TORSO HIP PELVIS NATURAL (284) DX TORSO SPINE (1408) DX TORSO SPINE CERVICAL (635) DX TORSO SPINE CERVICAL AP (230) DX TORSO SPINE CERVICAL LAT (405) DX TORSO SPINE LUMBAR (536) DX TORSO SPINE LUMBAR AP (288) DX TORSO SPINE LUMBAR LAT (248) DX TORSO SPINE THORACIC (237) DX TORSO SPINE THORACIC AP (117) DX TORSO SPINE THORACIC LAT (120) ECG (904) 3
5 4 ECG FIBRILLATION (566) ECG NORMAL (338) MR (1042) MR APPENDAGE (347) MR BRAIN (414) MR BRAIN AXIAL (259) MR BRAIN AXIAL COLLAGE (103) MR BRAIN AXIAL SINGLE (156) MR BRAIN SAGITTAL (155) MR HIP (100) MR KNEE (347) MR SPINE (181) PET (245) PET BW (134) PET COLOR (111) SM (334) SM BLOODSMEAR (334) SM BLOODSMEAR NORMAL (288) SM BLOODSMEAR SICKLECELL (46) US (400) US CARDIAC (190) US FETUS (210) 3 Abbreviations AP: Anterior-posterior view BW: Grayscale color spectrum CT: Computed Tomography DX: Digital X-Ray ECG: Electrocardiogram LAT: Lateral view MR: Magnetic Resonance OBL: Oblique PET: Positron Emmission Tomography SM: Slide Microscopy US: Ultrasound References 1. Cao, L., Codella, N., Connell, J., Merler, M., Nguyen, Q., Pankanti, S., Smith, J., IBM Multimedia ImageCLEF2013 ImageCLEF 2013 Medical Image Retrieval Workshop 2. Seco de Herrera, A.G., Kalpathy-Cramer, J., Fushman, D.D., Antani, S., Muller, H., Overview of the ImageCLEF 2013 medical tasks, ImageCLEF 2013 Medical Image Retrieval Workshop, 3. Image Retrieval in Medical Applications en.php 4. The Cancer Imaging Archive (TCIA)
6 5. Armato SG III, McLennan G, Bidaut L, McNitt-Gray MF, Meyer CR, Reeves AP, Zhao B, Aberle DR, Henschke CI, Hoffman EA, Kazerooni EA, MacMahon H, van Beek EJR, Yankelevitz D, et al. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI): A completed reference database of lung nodules on CT scans. Medical Physics, 38: , Cornell University Vision and Analysis Group SIMBA Dataset 7. Japanese Society of Radiological Technology 5
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