Difference between revisions of "Projects:QIN:3D Slicer Annotation Image Markup:Standard Terminology"
From NAMIC Wiki
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** http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=3407 | ** http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=3407 | ||
** http://bioportal.bioontology.org/ontologies/46836?p=terms&conceptid=D003560 | ** http://bioportal.bioontology.org/ontologies/46836?p=terms&conceptid=D003560 | ||
| + | * NeuroLex: http://neurolex.org/wiki/Main_Page (Karl Helmer from MGH used it and can help with the translation effort) | ||
| + | |||
==Original labels categorized== | ==Original labels categorized== | ||
Revision as of 18:00, 18 September 2012
Home < Projects:QIN:3D Slicer Annotation Image Markup:Standard TerminologyThis is a collection of relevant pieces from:
Contents
Segmentation image module attributes
Segmentation image module attributes must in particular include the following (PS 3.3-2011, p.989):
Code sequence attributes
General Anatomy Macro
The General Anatomy Macro is defined as follows (PS 3.3-2011, p.96):
Coding Scheme Designators
NOTE: this table is incomplete, consult PS 3.16-2011 p.43.
RadLex
- General information: http://rsna.org/RadLex.aspx
- License: http://rsna.org/uploadedFiles/RSNA/Content/Informatics/radlex_public_license_version_1-0-1.pdf
- Example hierarchy of the term mapping from RadLex browser (liver: http://www.radlex.org/RID/RID13419):
SNOMED
David Clunie in email communication Sept 17, 2012:
[...] The [DICOM] agreement with SNOMED is to allow any implementer to use the terms included in DICOM in their implementations and products without fee; it is not just to be able to include them in the text of the standard documents. So, since Slicer would be using the concepts to include in a DICOM SEG object, you do not need any additional agreement, nor any agreement with SNOMED to distribute the source code (my PixelMed Java DICOM toolkit is full of SNOMED codes, for example, and I neither have not need such an additional agreement).
Notes on choosing SNOMED concepts when fleshing out the table, esp. regarding anatomy. Make sure that you choose "(body structure)" concepts for anatomy, and that you pick the "entire ..." concept rather than "structure of" etc., and if the choice is not obvious, include about your choice so that these can be flagged for special attention during review.
One way to find the right SNOMED code without using one of the terminology browsers is just to download the text files from the UMLS (from http://www.nlm.nih.gov/research/umls/licensedcontent/snomedctfiles.html). You will need to register and get a user name and password.
Then you can use grep as follows:
% grep -i 'frontal lobe' sct1_Concepts_Core_INT_20110131.txt | grep -i structure | grep -i entire 180920004 0 Entire frontal lobe (body structure) 7N000 T-A2218 1 279169003 0 Entire frontal lobe gyrus (body structure) Xa10B T-A2207 1 314141005 0 Entire right frontal lobe (body structure) XaEYz T-A2213 0 314142003 0 Entire left frontal lobe (body structure) XaEZ0 T-A2214 0 362330001 0 Entire cortex of frontal lobe (body structure) XU96w T-A2211 1 362331002 0 Entire white matter of frontal lobe (body structure) XU96y T-A2221 1
You can find this sort of thing using the UMLS Terminology Browser (at https://uts.nlm.nih.gov/metathesaurus.html), for example, as follows:
Mapping Slicer GeneralAnatomy LUT to Standard Terminology (work in progress)
Original GeneralAnatomy LUT see here: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors
Standing issues: licensing and redistribution
TODO items: consider using alternative terminology vocabularies (will add corresponding columns):
- FMA
- browser http://fme.biostr.washington.edu/FME/
- available under CreativeCommons license: http://sig.biostr.washington.edu/projects/fm/index.html http://sig.biostr.washington.edu/projects/fma/release/index.html
- Medical Subject Headings (MeSH)
- NeuroLex: http://neurolex.org/wiki/Main_Page (Karl Helmer from MGH used it and can help with the translation effort)
Original labels categorized
| integer_label | text_label | color | notes | anatomic region | anatomic region modifier | primary anatomic structure | primary anatomic structure modifier | segmented property category - CID 7150 | segmented property type | segmented property type modifier |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | background | rgba(0,0,0,0) | ||||||||
| 1 | tissue | rgb(128,174,128) | Default label for bodily tissues | (T-D0050,SRT,"Tissue") | ||||||
| 2 | bone | rgb(241,214,145) | (T-D0050,SRT,"Tissue") | (T-D016E,SRT,"Bone") | ||||||
| 3 | skin | rgb(177,122,101) | ||||||||
| 4 | connective tissue | rgb(111,184,210) | ||||||||
| 5 | blood | rgb(216,101,79) | ||||||||
| 6 | organ | rgb(221,130,101) | ||||||||
| 7 | mass | rgb(144,238,144) | Could be tumor or other lesion | (M-01000,SRT,"Morphologically Altered Structure") | (M-03000,SRT,"Mass") - CID 7159++ | |||||
| 8 | muscle | rgb(192,104,88) | (T-D0050,SRT,"Tissue") | (T-13001,SRT,"Muscle") - CID 7160 (should refactor) | ||||||
| 9 | foreign object | rgb(220,245,20) | Implants, surical instruments, table... | (A-00004,SRT,"Physical Object") | (M-30400,SRT,"Foreign Body") | |||||
| 10 | waste | rgb(78,63,0) | ||||||||
| 11 | teeth | rgb(255,250,220) | ||||||||
| 12 | fat | rgb(230,220,70) | ||||||||
| 13 | gray matter | rgb(200,200,235) | cf. 39 and 116 | (T-D0050,SRT,"Tissue") | (T-A0096,SRT,"Gray Matter") - CID 7153 Edited | |||||
| 14 | white matter | rgb(250,250,210) | (T-D0050,SRT,"Tissue") | (T-A0095,SRT,"White Matter") - CID 7153 Edited | ||||||
| 15 | nerve | rgb(244,214,49) | ||||||||
| 16 | vein | rgb(0,151,206) | ||||||||
| 17 | artery | rgb(216,101,79) | ||||||||
| 18 | capillary | rgb(183,156,220) | ||||||||
| 19 | ligament | rgb(183,214,211) | ||||||||
| 20 | tendon | rgb(152,189,207) | ||||||||
| 21 | cartilage | rgb(111,184,210) | ||||||||
| 22 | meniscus | rgb(178,212,242) | ||||||||
| 23 | lymph node | rgb(68,172,100) | ||||||||
| 24 | lymphatic vessel | rgb(111,197,131) | ||||||||
| 25 | cerebro-spinal fluid | rgb(85,188,255) | cf. 106 | (T-D0050,SRT,"Tissue") | (T-A1000,SRT,"Cerebrospinal Fluid") - CID 7153 | |||||
| 26 | bile | rgb(0,145,30) | ||||||||
| 27 | urine | rgb(214,230,130) | ||||||||
| 28 | feces | rgb(78,63,0) | ||||||||
| 29 | gas | rgb(218,255,255) | ||||||||
| 30 | fluid | rgb(170,250,250) | ||||||||
| 31 | edema | rgb(140,224,228) | (M-01000,SRT,"Morphologically Altered Structure") | (M-36300,SRT,"Edema") - CID 7159++ | ||||||
| 32 | bleeding | rgb(188,65,28) | (M-01000,SRT,"Morphologically Altered Structure") | (M-37000,SRT,"Hemorrhage") - CID 7159++ | ||||||
| 33 | necrosis | rgb(216,191,216) | (M-01000,SRT,"Morphologically Altered Structure") | (M-54000,SRT,"Necrosis") - CID 7159 | ||||||
| 34 | clot | rgb(145,60,66) | (M-01000,SRT,"Morphologically Altered Structure") | (M-35000,SRT,"Blood Clot") - CID 7159++ | ||||||
| 35 | embolism | rgb(150,98,83) | (M-01000,SRT,"Morphologically Altered Structure") | (M-35300,SRT,"Embolus") - CID 7159++ | ||||||
| 36 | head | rgb(177,122,101) | ||||||||
| 37 | central nervous system | rgb(244,214,49) | ||||||||
| 38 | brain | rgb(250,250,225) | ? tissue or structure | (T-A0100,SRT,"Brain") - CID 7153++ | ||||||
| 39 | gray matter of brain | rgb(200,200,215) | cf. 13 and 116 | (T-D0050,SRT,"Tissue") | (T-A2020,SRT,"Cerebral Gray Matter") - CID 7153 Edited | |||||
| 40 | telencephalon | rgb(68,131,98) | ||||||||
| 41 | cerebral cortex | rgb(128,174,128) | ||||||||
| 42 | right frontal lobe | rgb(83,146,164) | (T-D000A,SRT,"Anatomical Structure") | (T-A2218,SRT,"Frontal Lobe") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 43 | left frontal lobe | rgb(83,146,164) | (T-D000A,SRT,"Anatomical Structure") | (T-A2218,SRT,"Frontal Lobe") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 44 | right temporal lobe | rgb(162,115,105) | (T-D000A,SRT,"Anatomical Structure") | (T-A2513,SRT,"Temporal Lobe") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 45 | left temporal lobe | rgb(162,115,105) | (T-D000A,SRT,"Anatomical Structure") | (T-A2513,SRT,"Temporal Lobe") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 46 | right parietal lobe | rgb(141,93,137) | (T-D000A,SRT,"Anatomical Structure") | (T-A230F,SRT,"Parietal Lobe") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 47 | left parietal lobe | rgb(141,93,137) | (T-D000A,SRT,"Anatomical Structure") | (T-A230F,SRT,"Parietal Lobe") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 48 | right occipital lobe | rgb(182,166,110) | (T-D000A,SRT,"Anatomical Structure") | (T-A240F,SRT,"Occipital Lobe") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 49 | left occipital lobe | rgb(182,166,110) | (T-D000A,SRT,"Anatomical Structure") | (T-A240F,SRT,"Occipital Lobe") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 50 | right insular lobe | rgb(188,135,166) | (T-D000A,SRT,"Anatomical Structure") | (T-A2615,SRT,"Insula") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 51 | left insular lobe | rgb(188,135,166) | (T-D000A,SRT,"Anatomical Structure") | (T-A2615,SRT,"Insula") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 52 | right limbic lobe | rgb(154,150,201) | (T-D000A,SRT,"Anatomical Structure") | (T-A0036,SRT,"Limbic Lobe") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 53 | left limbic lobe | rgb(154,150,201) | (T-D000A,SRT,"Anatomical Structure") | (T-A0036,SRT,"Limbic Lobe") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 54 | right striatum | rgb(177,140,190) | ||||||||
| 55 | left striatum | rgb(177,140,190) | ||||||||
| 56 | right caudate nucleus | rgb(30,111,85) | (T-D000A,SRT,"Anatomical Structure") | (T-A3201,SRT,"Caudate Nucleus") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 57 | left caudate nucleus | rgb(30,111,85) | (T-D000A,SRT,"Anatomical Structure") | (T-A3201,SRT,"Caudate Nucleus") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 58 | right putamen | rgb(210,157,166) | ||||||||
| 59 | left putamen | rgb(210,157,166) | ||||||||
| 60 | right pallidum | rgb(48,129,126) | ||||||||
| 61 | left pallidum | rgb(48,129,126) | ||||||||
| 62 | right amygdaloid complex | rgb(98,153,112) | ||||||||
| 63 | left amygdaloid complex | rgb(98,153,112) | ||||||||
| 64 | diencephalon | rgb(69,110,53) | ||||||||
| 65 | thalamus | rgb(166,113,137) | ||||||||
| 66 | right thalamus | rgb(122,101,38) | ||||||||
| 67 | left thalamus | rgb(122,101,38) | ||||||||
| 68 | pineal gland | rgb(253,135,192) | ||||||||
| 69 | midbrain | rgb(145,92,109) | ||||||||
| 70 | substantia nigra | rgb(46,101,131) | ||||||||
| 71 | right substantia nigra | rgb(0,108,112) | ||||||||
| 72 | left substantia nigra | rgb(0,108,112) | ||||||||
| 73 | cerebral white matter | rgb(250,250,225) | ||||||||
| 74 | right superior longitudinal fasciculus | rgb(127,150,88) | (T-D000A,SRT,"Anatomical Structure") | (T-A2820,SRT,"Superior Longitudinal Fasciculus") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 75 | left superior longitudinal fasciculus | rgb(127,150,88) | (T-D000A,SRT,"Anatomical Structure") | (T-A2820,SRT,"Superior Longitudinal Fasciculus") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 76 | right inferior longitudinal fasciculus | rgb(159,116,163) | ||||||||
| 77 | left inferior longitudinal fasciculus | rgb(159,116,163) | ||||||||
| 78 | right arcuate fasciculus | rgb(125,102,154) | DC: SNOMED needs fixing - specifies arcuate as synonym (ratehr than part of) superior longitudinal fasciculus | (T-D000A,SRT,"Anatomical Structure") | (276650,FMA,"Arcuate Fasciculus") - CID 7153++ | (G-A100,SRT,"Right") | ||||
| 79 | left arcuate fasciculus | rgb(125,102,154) | (T-D000A,SRT,"Anatomical Structure") | (276650,FMA,"Arcuate Fasciculus") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 80 | right uncinate fasciculus | rgb(106,174,155) | (T-D000A,SRT,"Anatomical Structure") | (T-A2831,SRT,"Uncinate Fasciculus") - CID 7153++ | (G-A100,SRT,"Right") | |||||
| 81 | left uncinate fasciculus | rgb(106,174,155) | (T-D000A,SRT,"Anatomical Structure") | (T-A2831,SRT,"Uncinate Fasciculus") - CID 7153++ | (G-A101,SRT,"Left") | |||||
| 82 | right cingulum bundle | rgb(154,146,83) | ||||||||
| 83 | left cingulum bundle | rgb(154,146,83) | ||||||||
| 84 | projection fibers | rgb(126,126,55) | ||||||||
| 85 | right corticospinal tract | rgb(201,160,133) | ||||||||
| 86 | left corticospinal tract | rgb(201,160,133) | ||||||||
| 87 | right optic radiation | rgb(78,152,141) | ||||||||
| 88 | left optic radiation | rgb(78,152,141) | ||||||||
| 89 | right medial lemniscus | rgb(174,140,103) | ||||||||
| 90 | left medial lemniscus | rgb(174,140,103) | ||||||||
| 91 | right superior cerebellar peduncle | rgb(139,126,177) | ||||||||
| 92 | left superior cerebellar peduncle | rgb(139,126,177) | ||||||||
| 93 | right middle cerebellar peduncle | rgb(148,120,72) | ||||||||
| 94 | left middle cerebellar peduncle | rgb(148,120,72) | ||||||||
| 95 | right inferior cerebellar peduncle | rgb(186,135,135) | ||||||||
| 96 | left inferior cerebellar peduncle | rgb(186,135,135) | ||||||||
| 97 | optic chiasm | rgb(99,106,24) | ||||||||
| 98 | right optic tract | rgb(156,171,108) | ||||||||
| 99 | left optic tract | rgb(156,171,108) | ||||||||
| 100 | right fornix | rgb(64,123,147) | ||||||||
| 101 | left fornix | rgb(64,123,147) | ||||||||
| 102 | commissural fibers | rgb(138,95,74) | ||||||||
| 103 | corpus callosum | rgb(97,113,158) | ||||||||
| 104 | posterior commissure | rgb(126,161,197) | ||||||||
| 105 | cerebellar white matter | rgb(194,195,164) | (T-A6080,SRT,"Cerebellar White Matter") - CID 7153++ | |||||||
| 106 | CSF space | rgb(85,188,255) | DC: cf. 25; is this one supposed to be brain-specific? assume so | (T-A0109,SRT,"Brain Cerebrospinal Fluid Pathway") - CID 7153++ | ||||||
| 107 | ventricles of brain | rgb(88,106,215) | ||||||||
| 108 | right lateral ventricle | rgb(88,106,215) | ||||||||
| 109 | left lateral ventricle | rgb(88,106,215) | ||||||||
| 110 | right third ventricle | rgb(88,106,215) | ||||||||
| 111 | left third ventricle | rgb(88,106,215) | ||||||||
| 112 | cerebral aqueduct | rgb(88,106,215) | ||||||||
| 113 | fourth ventricle | rgb(88,106,215) | ||||||||
| 114 | subarachnoid space | rgb(88,106,215) | ||||||||
| 115 | spinal cord | rgb(244,214,49) | ||||||||
| 116 | gray matter of spinal cord | rgb(200,200,215) | cf. 7 and 39 | (T-A7020,SRT,"Spinal Cord Gray Matter") - CID 7153++ | ||||||
| 117 | white matter of spinal cord | rgb(250,250,225) | (T-A7070,SRT,"Spinal Cord White Matter") - CID 7153++ | |||||||
| 118 | endocrine system of brain | rgb(82,174,128) | ||||||||
| 119 | pituitary gland | rgb(57,157,110) | ||||||||
| 120 | adenohypophysis | rgb(60,143,83) | ||||||||
| 121 | neurohypophysis | rgb(92,162,109) | ||||||||
| 122 | meninges | rgb(255,244,209) | (T-A1110,SRT,"Meninges") - CID 7153 | |||||||
| 123 | dura mater | rgb(255,244,209) | ||||||||
| 124 | arachnoid | rgb(255,244,209) | ||||||||
| 125 | pia mater | rgb(255,244,209) | ||||||||
| 126 | muscles of head | rgb(201,121,77) | ||||||||
| 127 | salivary glands | rgb(70,163,117) | ||||||||
| 128 | lips | rgb(188,91,95) | ||||||||
| 129 | nose | rgb(177,122,101) | ||||||||
| 130 | tongue | rgb(166,84,94) | ||||||||
| 131 | soft palate | rgb(182,105,107) | ||||||||
| 132 | right inner ear | rgb(229,147,118) | ||||||||
| 133 | left inner ear | rgb(229,147,118) | ||||||||
| 134 | right external ear | rgb(174,122,90) | ||||||||
| 135 | left external ear | rgb(174,122,90) | ||||||||
| 136 | right middle ear | rgb(201,112,73) | ||||||||
| 137 | left middle ear | rgb(201,112,73) | ||||||||
| 138 | right eyeball | rgb(194,142,0) | ||||||||
| 139 | left eyeball | rgb(194,142,0) | ||||||||
| 140 | skull | rgb(241,213,144) | (T-11100,SRT,"Skull") - CID 7153 | |||||||
| 141 | right frontal bone | rgb(203,179,77) | ||||||||
| 142 | left frontal bone | rgb(203,179,77) | ||||||||
| 143 | right parietal bone | rgb(229,204,109) | ||||||||
| 144 | left parietal bone | rgb(229,204,109) | ||||||||
| 145 | right temporal bone | rgb(255,243,152) | ||||||||
| 146 | left temporal bone | rgb(255,243,152) | ||||||||
| 147 | right sphenoid bone | rgb(209,185,85) | ||||||||
| 148 | left sphenoid bone | rgb(209,185,85) | ||||||||
| 149 | right ethmoid bone | rgb(248,223,131) | ||||||||
| 150 | left ethmoid bone | rgb(248,223,131) | ||||||||
| 151 | occipital bone | rgb(255,230,138) | ||||||||
| 152 | maxilla | rgb(196,172,68) | ||||||||
| 153 | right zygomatic bone | rgb(255,255,167) | DC: ? use more general (T-111BE,SRT,"Zygoma"); also, where is the left one ?? | (T-11167,SRT,"Zygomatic arch") - CID 4028 | (G-A100,SRT,"Right") | |||||
| 154 | right lacrimal bone | rgb(255,250,160) | ||||||||
| 155 | vomer bone | rgb(255,237,145) | ||||||||
| 156 | right palatine bone | rgb(242,217,123) | (T-111A8,SRT,"Palatine Bone") | (G-A100,SRT,"Right") | ||||||
| 157 | left palatine bone | rgb(242,217,123) | (T-111A8,SRT,"Palatine Bone") | (G-A101,SRT,"Left") | ||||||
| 158 | mandible | rgb(222,198,101) | ||||||||
| 159 | neck | rgb(177,122,101) | ||||||||
| 160 | muscles of neck | rgb(213,124,109) | ||||||||
| 161 | pharynx | rgb(184,105,108) | ||||||||
| 162 | larynx | rgb(150,208,243) | ||||||||
| 163 | thyroid gland | rgb(62,162,114) | ||||||||
| 164 | right parathyroid glands | rgb(62,162,114) | ||||||||
| 165 | left parathyroid glands | rgb(62,162,114) | ||||||||
| 166 | skeleton of neck | rgb(242,206,142) | ||||||||
| 167 | hyoid bone | rgb(250,210,139) | ||||||||
| 168 | cervical vertebral column | rgb(255,255,207) | ||||||||
| 169 | thorax | rgb(177,122,101) | ||||||||
| 170 | trachea | rgb(182,228,255) | ||||||||
| 171 | bronchi | rgb(175,216,244) | (T-D000A,SRT,"Anatomical Structure") | (T-26000,SRT,"Bronchi") - CID 7155 | ||||||
| 172 | right lung | rgb(197,165,145) | (T-D000A,SRT,"Anatomical Structure") | (T-28000,SRT,"Lung") - CID 7155 | (G-A100,SRT,"Right") | |||||
| 173 | left lung | rgb(197,165,145) | (T-D000A,SRT,"Anatomical Structure") | (T-28000,SRT,"Lung") - CID 7155 | (G-A101,SRT,"Left") | |||||
| 174 | superior lobe of right lung | rgb(172,138,115) | ||||||||
| 175 | superior lobe of left lung | rgb(172,138,115) | ||||||||
| 176 | middle lobe of right lung | rgb(202,164,140) | ||||||||
| 177 | inferior lobe of right lung | rgb(224,186,162) | ||||||||
| 178 | inferior lobe of left lung | rgb(224,186,162) | ||||||||
| 179 | pleura | rgb(255,245,217) | ||||||||
| 180 | heart | rgb(206,110,84) | (T-D000A,SRT,"Anatomical Structure") | (T-32000,SRT,"Heart") - CID 7152 | ||||||
| 181 | right atrium | rgb(210,115,89) | ||||||||
| 182 | left atrium | rgb(203,108,81) | ||||||||
| 183 | atrial septum | rgb(233,138,112) | ||||||||
| 184 | ventricular septum | rgb(195,100,73) | ||||||||
| 185 | right ventricle of heart | rgb(181,85,57) | DC: SRT code is precordinated; no need for laterality modifier | (T-D000A,SRT,"Anatomical Structure") | (T-32500,SRT,"Right Ventricle") - CID 7152 | |||||
| 186 | left ventricle of heart | rgb(152,55,13) | DC: SRT code is precordinated; no need for laterality modifier | (T-D000A,SRT,"Anatomical Structure") | (T-32600,SRT,"Left Ventricle") - CID 7152 | |||||
| 187 | mitral valve | rgb(159,63,27) | ||||||||
| 188 | tricuspid valve | rgb(166,70,38) | ||||||||
| 189 | aortic valve | rgb(218,123,97) | ||||||||
| 190 | pulmonary valve | rgb(225,130,104) | ||||||||
| 191 | aorta | rgb(224,97,76) | DC: ? need specific parts (ascending, arch, descending thoracic, abdominal) | (T-D000A,SRT,"Anatomical Structure") | (T-42000,SRT,"Aorta") - CID 7152 | |||||
| 192 | pericardium | rgb(255,244,209) | ||||||||
| 193 | pericardial cavity | rgb(184,122,154) | ||||||||
| 194 | esophagus | rgb(211,171,143) | ||||||||
| 195 | thymus | rgb(47,150,103) | ||||||||
| 196 | mediastinum | rgb(255,244,209) | ||||||||
| 197 | skin of thoracic wall | rgb(173,121,88) | ||||||||
| 198 | muscles of thoracic wall | rgb(188,95,76) | ||||||||
| 199 | skeleton of thorax | rgb(255,239,172) | ||||||||
| 200 | thoracic vertebral column | rgb(226,202,134) | ||||||||
| 201 | ribs | rgb(253,232,158) | ||||||||
| 202 | sternum | rgb(244,217,154) | ||||||||
| 203 | right clavicle | rgb(205,179,108) | ||||||||
| 204 | left clavicle | rgb(205,179,108) | ||||||||
| 205 | abdominal cavity | rgb(186,124,161) | ||||||||
| 206 | abdomen | rgb(177,122,101) | ||||||||
| 207 | peritoneum | rgb(255,255,220) | ||||||||
| 208 | omentum | rgb(234,234,194) | ||||||||
| 209 | peritoneal cavity | rgb(204,142,178) | ||||||||
| 210 | retroperitoneal space | rgb(180,119,153) | ||||||||
| 211 | stomach | rgb(216,132,105) | ||||||||
| 212 | duodenum | rgb(255,253,229) | ||||||||
| 213 | small bowel | rgb(205,167,142) | ||||||||
| 214 | colon | rgb(204,168,143) | ||||||||
| 215 | anus | rgb(255,224,199) | ||||||||
| 216 | liver | rgb(221,130,101) | (T-D000A,SRT,"Anatomical Structure") | (T-62000,SRT,"Liver") - CID 7154 | ||||||
| 217 | biliary tree | rgb(0,145,30) | ||||||||
| 218 | gallbladder | rgb(139,150,98) | ||||||||
| 219 | pancreas | rgb(249,180,111) | ||||||||
| 220 | spleen | rgb(157,108,162) | (T-D000A,SRT,"Anatomical Structure") | (T-C3000,SRT,"Spleen) - CID 7154 | ||||||
| 221 | urinary system | rgb(203,136,116) | ||||||||
| 222 | right kidney | rgb(185,102,83) | (T-D000A,SRT,"Anatomical Structure") | (T-71000,SRT,"Kidney") - CID 7154 | (G-A100,SRT,"Right") | |||||
| 223 | left kidney | rgb(185,102,83) | (T-D000A,SRT,"Anatomical Structure") | (T-71000,SRT,"Kidney") - CID 7154 | (G-A101,SRT,"Left") | |||||
| 224 | right ureter | rgb(247,182,164) | ||||||||
| 225 | left ureter | rgb(247,182,164) | ||||||||
| 226 | urinary bladder | rgb(222,154,132) | ||||||||
| 227 | urethra | rgb(124,186,223) | ||||||||
| 228 | right adrenal gland | rgb(249,186,150) | (T-D000A,SRT,"Anatomical Structure") | (T-B3000,SRT,"Adrenal Gland") | (G-A100,SRT,"Right") | |||||
| 229 | left adrenal gland | rgb(249,186,150) | (T-D000A,SRT,"Anatomical Structure") | (T-B3000,SRT,"Adrenal Gland") | (G-A101,SRT,"Left") | |||||
| 230 | female internal genitalia | rgb(244,170,147) | ||||||||
| 231 | uterus | rgb(255,181,158) | ||||||||
| 232 | right fallopian tube | rgb(255,190,165) | ||||||||
| 233 | left fallopian tube | rgb(227,153,130) | ||||||||
| 234 | right ovary | rgb(213,141,113) | ||||||||
| 235 | left ovary | rgb(213,141,113) | ||||||||
| 236 | vagina | rgb(193,123,103) | ||||||||
| 237 | male internal genitalia | rgb(216,146,127) | ||||||||
| 238 | prostate | rgb(230,158,140) | ||||||||
| 239 | right seminal vesicle | rgb(245,172,147) | ||||||||
| 240 | left seminal vesicle | rgb(245,172,147) | ||||||||
| 241 | right deferent duct | rgb(241,172,151) | ||||||||
| 242 | left deferent duct | rgb(241,172,151) | ||||||||
| 243 | skin of abdominal wall | rgb(177,124,92) | ||||||||
| 244 | muscles of abdominal wall | rgb(171,85,68) | ||||||||
| 245 | skeleton of abdomen | rgb(217,198,131) | ||||||||
| 246 | lumbar vertebral column | rgb(212,188,102) | ||||||||
| 247 | female external genitalia | rgb(185,135,134) | ||||||||
| 248 | male external genitalia | rgb(185,135,134) | ||||||||
| 249 | skeleton of upper limb | rgb(198,175,125) | ||||||||
| 250 | muscles of upper limb | rgb(194,98,79) | ||||||||
| 251 | right upper limb | rgb(177,122,101) | ||||||||
| 252 | left upper limb | rgb(177,122,101) | ||||||||
| 253 | right shoulder | rgb(177,122,101) | ||||||||
| 254 | left shoulder | rgb(177,122,101) | ||||||||
| 255 | right arm | rgb(177,122,101) | ||||||||
| 256 | left arm | rgb(177,122,101) | ||||||||
| 257 | right elbow | rgb(177,122,101) | ||||||||
| 258 | left elbow | rgb(177,122,101) | ||||||||
| 259 | right forearm | rgb(177,122,101) | ||||||||
| 260 | left forearm | rgb(177,122,101) | ||||||||
| 261 | right wrist | rgb(177,122,101) | ||||||||
| 262 | left wrist | rgb(177,122,101) | ||||||||
| 263 | right hand | rgb(177,122,101) | ||||||||
| 264 | left hand | rgb(177,122,101) | ||||||||
| 265 | skeleton of lower limb | rgb(255,238,170) | ||||||||
| 266 | muscles of lower limb | rgb(206,111,93) | ||||||||
| 267 | right lower limb | rgb(177,122,101) | ||||||||
| 268 | left lower limb | rgb(177,122,101) | ||||||||
| 269 | right hip | rgb(177,122,101) | ||||||||
| 270 | left hip | rgb(177,122,101) | ||||||||
| 271 | right thigh | rgb(177,122,101) | ||||||||
| 272 | left thigh | rgb(177,122,101) | ||||||||
| 273 | right knee | rgb(177,122,101) | ||||||||
| 274 | left knee | rgb(177,122,101) | ||||||||
| 275 | right leg | rgb(177,122,101) | ||||||||
| 276 | left leg | rgb(177,122,101) | ||||||||
| 277 | right foot | rgb(177,122,101) | ||||||||
| 278 | left foot | rgb(177,122,101) | ||||||||
| 279 | peripheral nervous system | rgb(216,186,0) | ||||||||
| 280 | autonomic nerve | rgb(255,226,77) | ||||||||
| 281 | sympathetic trunk | rgb(255,243,106) | ||||||||
| 282 | cranial nerves | rgb(255,234,92) | ||||||||
| 283 | vagus nerve | rgb(240,210,35) | ||||||||
| 284 | peripheral nerve | rgb(224,194,0) | ||||||||
| 285 | circulatory system | rgb(213,99,79) | ||||||||
| 286 | systemic arterial system | rgb(217,102,81) | ||||||||
| 287 | systemic venous system | rgb(0,147,202) | ||||||||
| 288 | pulmonary arterial system | rgb(0,122,171) | ||||||||
| 289 | pulmonary venous system | rgb(186,77,64) | ||||||||
| 290 | lymphatic system | rgb(111,197,131) | ||||||||
| 291 | needle | rgb(240,255,30) | (A-00004,SRT,"Physical Object") | (A-30360,SRT,"Needle") - CID 7157++ | ||||||
| 292 | region 0 | rgb(185,232,61) | ||||||||
| 293 | region 1 | rgb(0,226,255) | ||||||||
| 294 | region 2 | rgb(251,159,255) | ||||||||
| 295 | region 3 | rgb(230,169,29) | ||||||||
| 296 | region 4 | rgb(0,194,113) | ||||||||
| 297 | region 5 | rgb(104,160,249) | ||||||||
| 298 | region 6 | rgb(221,108,158) | ||||||||
| 299 | region 7 | rgb(137,142,0) | ||||||||
| 300 | region 8 | rgb(230,70,0) | ||||||||
| 301 | region 9 | rgb(0,147,0) | ||||||||
| 302 | region 10 | rgb(0,147,248) | ||||||||
| 303 | region 11 | rgb(231,0,206) | ||||||||
| 304 | region 12 | rgb(129,78,0) | ||||||||
| 305 | region 13 | rgb(0,116,0) | ||||||||
| 306 | region 14 | rgb(0,0,255) | ||||||||
| 307 | region 15 | rgb(157,0,0) | ||||||||
| 308 | unknown | rgb(100,100,130) | ||||||||
| 309 | cyst | rgb(205,205,100) | (M-01000,SRT,"Morphologically Altered Structure") | (M-3340A,SRT,"Cyst") - CID 7159 |
New labels added
| integer_label | text_label | color | notes | anatomic region | anatomic region modifier | primary anatomic structure | primary anatomic structure modifier | segmented property category - CID 7150 | segmented property type | segmented property type modifier |
|---|---|---|---|---|---|---|---|---|---|---|
| ?? | rectum | rgba(?,?,?,?) | (M-01000,SRT,"Morphologically Altered Structure") | (M-3340A,SRT,"Cyst") - CID 7159 | ||||||
| ?? | left testis | rgba(?,?,?,?) | (T-D000A,SRT,"Anatomical Structure") | (T-94000,SRT,"Testis") - CID 7160 | ||||||
| ?? | right testis | rgba(?,?,?,?) | (T-D000A,SRT,"Anatomical Structure") | (T-94000,SRT,"Testis") - CID 7160 | ||||||
| ?? | cervix | rgba(?,?,?,?) | (T-D000A,SRT,"Anatomical Structure") | (T-83200,SRT,"Cervix") - CID 7160 | ||||||
| ?? | diaphragm | rgba(?,?,?,?) | DC: ? need left/right - probably not | (T-D000A,SRT,"Anatomical Structure") | (T-D3400,SRT,"Diaphragm) - CID 7155 | |||||
| ?? | table | rgba(?,?,?,?) | DC: cf. 9 - table detection is handled specifically by some systems | (A-00004,SRT,"Physical Object") | (A-17350,SRT,"Table") - CID 7158 | |||||
| ?? | clothing | rgba(?,?,?,?) | cf. 9 | (A-00004,SRT,"Physical Object") | (A-00916,SRT,"Clothing") - CID 7158 |
Segmentation objects allow to encode recommended display color in "Recommended Display CIELab Value" (0062,000D) attribute; these values are encoded in CIALab.
