bdsa-react-components 0.1.21 → 0.1.25

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Files changed (74) hide show
  1. package/CHANGELOG.md +31 -0
  2. package/CURSOR_INTEGRATION.md +25 -3
  3. package/INTEGRATION.md +0 -0
  4. package/README.md +0 -0
  5. package/dist/auth/DsaAuthProvider.d.ts +92 -0
  6. package/dist/auth/DsaAuthProvider.d.ts.map +1 -0
  7. package/dist/auth/DsaAuthStore.d.ts +5 -0
  8. package/dist/auth/DsaAuthStore.d.ts.map +1 -1
  9. package/dist/auth/index.d.ts +3 -1
  10. package/dist/auth/index.d.ts.map +1 -1
  11. package/dist/auth/types.d.ts +43 -0
  12. package/dist/auth/types.d.ts.map +1 -1
  13. package/dist/bdsa-schema.json +896 -0
  14. package/dist/components/DsaAuthManager/DsaAuthManager.d.ts +49 -4
  15. package/dist/components/DsaAuthManager/DsaAuthManager.d.ts.map +1 -1
  16. package/dist/components/DsaErrorBoundary/DsaErrorBoundary.d.ts +73 -0
  17. package/dist/components/DsaErrorBoundary/DsaErrorBoundary.d.ts.map +1 -0
  18. package/dist/components/DsaErrorBoundary/index.d.ts +3 -0
  19. package/dist/components/DsaErrorBoundary/index.d.ts.map +1 -0
  20. package/dist/components/FolderBrowser/FolderBrowser.d.ts.map +1 -1
  21. package/dist/components/FolderBrowser/FolderBrowser.types.d.ts +139 -2
  22. package/dist/components/FolderBrowser/FolderBrowser.types.d.ts.map +1 -1
  23. package/dist/components/FolderBrowser/useFolderBrowserDataFetching.d.ts +2 -0
  24. package/dist/components/FolderBrowser/useFolderBrowserDataFetching.d.ts.map +1 -1
  25. package/dist/components/FolderThumbnailBrowser/FolderThumbnailBrowser.d.ts +30 -0
  26. package/dist/components/FolderThumbnailBrowser/FolderThumbnailBrowser.d.ts.map +1 -1
  27. package/dist/components/ProtocolManager/ProtocolCard.d.ts +8 -0
  28. package/dist/components/ProtocolManager/ProtocolCard.d.ts.map +1 -0
  29. package/dist/components/ProtocolManager/ProtocolContext.d.ts +46 -0
  30. package/dist/components/ProtocolManager/ProtocolContext.d.ts.map +1 -0
  31. package/dist/components/ProtocolManager/ProtocolList.d.ts +8 -0
  32. package/dist/components/ProtocolManager/ProtocolList.d.ts.map +1 -0
  33. package/dist/components/ProtocolManager/ProtocolManager.d.ts +38 -0
  34. package/dist/components/ProtocolManager/ProtocolManager.d.ts.map +1 -0
  35. package/dist/components/ProtocolManager/ProtocolManager.types.d.ts +139 -0
  36. package/dist/components/ProtocolManager/ProtocolManager.types.d.ts.map +1 -0
  37. package/dist/components/ProtocolManager/ProtocolModal.d.ts +10 -0
  38. package/dist/components/ProtocolManager/ProtocolModal.d.ts.map +1 -0
  39. package/dist/components/ProtocolManager/ProtocolsTab.d.ts +10 -0
  40. package/dist/components/ProtocolManager/ProtocolsTab.d.ts.map +1 -0
  41. package/dist/components/ProtocolManager/adapters/DsaSyncAdapter.d.ts +76 -0
  42. package/dist/components/ProtocolManager/adapters/DsaSyncAdapter.d.ts.map +1 -0
  43. package/dist/components/ProtocolManager/storage/protocolStorage.d.ts +39 -0
  44. package/dist/components/ProtocolManager/storage/protocolStorage.d.ts.map +1 -0
  45. package/dist/components/ProtocolManager/testData.d.ts +23 -0
  46. package/dist/components/ProtocolManager/testData.d.ts.map +1 -0
  47. package/dist/components/ProtocolManager/utils/schemaValidator.d.ts +99 -0
  48. package/dist/components/ProtocolManager/utils/schemaValidator.d.ts.map +1 -0
  49. package/dist/components/SlideViewer/SlideViewer.d.ts +1 -1
  50. package/dist/components/SlideViewer/SlideViewer.d.ts.map +1 -1
  51. package/dist/components/SlideViewer/SlideViewer.types.d.ts +254 -21
  52. package/dist/components/SlideViewer/SlideViewer.types.d.ts.map +1 -1
  53. package/dist/components/SlideViewer/hooks/index.d.ts +2 -0
  54. package/dist/components/SlideViewer/hooks/index.d.ts.map +1 -1
  55. package/dist/components/SlideViewer/hooks/useAnnotationFetching.d.ts +2 -1
  56. package/dist/components/SlideViewer/hooks/useAnnotationFetching.d.ts.map +1 -1
  57. package/dist/components/SlideViewer/hooks/useOverlayTileSources.d.ts +9 -0
  58. package/dist/components/SlideViewer/hooks/useOverlayTileSources.d.ts.map +1 -0
  59. package/dist/components/SlideViewer/hooks/useViewportChange.d.ts +14 -0
  60. package/dist/components/SlideViewer/hooks/useViewportChange.d.ts.map +1 -0
  61. package/dist/components/ThumbnailGrid/ThumbnailGrid.d.ts +30 -0
  62. package/dist/components/ThumbnailGrid/ThumbnailGrid.d.ts.map +1 -1
  63. package/dist/index.cjs +55 -41
  64. package/dist/index.cjs.map +1 -1
  65. package/dist/index.d.ts +15 -1
  66. package/dist/index.d.ts.map +1 -1
  67. package/dist/index.js +19916 -17906
  68. package/dist/index.js.map +1 -1
  69. package/dist/style.css +1 -1
  70. package/dist/utils/apiErrorHandling.d.ts +44 -0
  71. package/dist/utils/apiErrorHandling.d.ts.map +1 -0
  72. package/dist/utils/patchOsdPaperjs.d.ts.map +1 -1
  73. package/package.json +3 -3
  74. package/patches/osd-paperjs-annotation+0.4.14.patch +0 -0
package/dist/bdsa-schema.json ADDED
@@ -0,0 +1,896 @@
1
+ {
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+ "$schema": "https://json-schema.org/draft/2020-12/schema",
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+ "$id": "https://example.com/product.schema.json",
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+ "title": "BDSA Schema",
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+ "description": "JSON Schema for the BDSA Project.",
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+ "type": "object",
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+ "required": [
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+ "bdsaID",
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+ "stainID",
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+ "regionIDs"
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+ ],
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+ "properties": {
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+ "bdsaID": {
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+ "type": "string",
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+ "title": "BDSA ID",
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+ "pattern": "^BDSA\\d+\\.\\d+$",
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+ "description": "Unique BDSA case identifier (example: \"BDSA1.33\")"
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+ },
19
+ "stainIDs": {
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+ "type": "array",
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+ "items": {
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+ "title": "Stain ID",
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+ "description": "Stain used on tissue section, with potentially additional information.",
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+ "properties": {
25
+ "TDP-43": {
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+ "type": "object",
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+ "title": "TDP-43",
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+ "abbreviation": "TDP",
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+ "required": [
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+ "phospho-specific"
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+ ],
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+ "properties": {
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+ "phospho-specific": {
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+ "type": "string",
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+ "title": "Phospho-specific",
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+ "enum": [
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+ "yes",
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+ "no"
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+ ]
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+ },
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+ "dilution": {
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+ "type": "string",
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+ "title": "Dilution",
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+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
45
+ "pattern": "^1:\\d+$",
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+ "examples": [
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+ "1:100",
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+ "1:1000"
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+ ]
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+ },
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+ "vendor": {
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+ "type": "string",
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+ "title": "Vendor"
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+ },
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+ "chromogen": {
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+ "type": "string",
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+ "title": "Chromogen",
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+ "default": "DAB (brown)",
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+ "enum": [
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+ "DAB (brown)",
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+ "AEC (red)",
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+ "Fast Red (red)",
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+ "NovaRED (red)",
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+ "VIP (purple)",
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+ "BCIP/NBT (blue)",
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+ "Other"
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+ ]
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+ }
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+ }
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+ },
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+ "aSyn": {
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+ "type": "object",
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+ "title": "Alpha Synuclein",
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+ "abbreviation": "aSyn",
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+ "required": [
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+ "phospho-specific"
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+ ],
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+ "properties": {
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+ "phospho-specific": {
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+ "type": "string",
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+ "title": "Phospho-specific",
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+ "enum": [
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+ "yes",
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+ "no"
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+ ]
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+ },
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+ "dilution": {
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+ "type": "string",
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+ "title": "Dilution",
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+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
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+ "pattern": "^1:\\d+$",
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+ "examples": [
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+ "1:100",
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+ "1:1000"
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+ ]
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+ },
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+ "vendor": {
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+ "type": "string",
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+ "title": "Vendor"
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+ },
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+ "chromogen": {
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+ "type": "string",
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+ "title": "Chromogen",
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+ "default": "DAB (brown)",
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+ "enum": [
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+ "DAB (brown)",
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+ "AEC (red)",
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+ "Fast Red (red)",
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+ "NovaRED (red)",
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+ "VIP (purple)",
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+ "BCIP/NBT (blue)",
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+ "Other"
113
+ ]
114
+ }
115
+ }
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+ },
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+ "HE": {
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+ "type": "object",
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+ "title": "Hematoxylin and Eosin",
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+ "abbreviation": "HE",
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+ "properties": {
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+ "dilution": {
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+ "type": "string",
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+ "title": "Dilution",
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+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
126
+ "pattern": "^1:\\d+$",
127
+ "examples": [
128
+ "1:100",
129
+ "1:1000"
130
+ ]
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+ },
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+ "vendor": {
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+ "type": "string",
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+ "title": "Vendor"
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+ }
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+ }
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+ },
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+ "Silver": {
139
+ "type": "object",
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+ "title": "Silver Stain",
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+ "abbreviation": "Silver",
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+ "required": [
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+ "technique"
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+ ],
145
+ "properties": {
146
+ "technique": {
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+ "type": "string",
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+ "title": "Silver Stain",
149
+ "enum": [
150
+ "Bielschowsky",
151
+ "Gallyas",
152
+ "Campbell-Switzer"
153
+ ]
154
+ },
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+ "dilution": {
156
+ "type": "string",
157
+ "title": "Dilution",
158
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
159
+ "pattern": "^1:\\d+$",
160
+ "examples": [
161
+ "1:100",
162
+ "1:1000"
163
+ ]
164
+ },
165
+ "vendor": {
166
+ "type": "string",
167
+ "title": "Vendor"
168
+ }
169
+ }
170
+ },
171
+ "Thioflavin": {
172
+ "type": "object",
173
+ "title": "Thioflavin",
174
+ "abbreviation": "ThioS"
175
+ },
176
+ "Tau": {
177
+ "type": "object",
178
+ "title": "Tau",
179
+ "abbreviation": "Tau",
180
+ "required": [
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+ "antibody"
182
+ ],
183
+ "properties": {
184
+ "antibody": {
185
+ "type": "string",
186
+ "title": "Antibody",
187
+ "enum": [
188
+ "AT8",
189
+ "PHF1",
190
+ "CP13",
191
+ "Total Tau",
192
+ "RD3",
193
+ "RD4"
194
+ ]
195
+ },
196
+ "vendor": {
197
+ "type": "string",
198
+ "title": "Vendor"
199
+ },
200
+ "dilution": {
201
+ "type": "string",
202
+ "title": "Dilution",
203
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
204
+ "pattern": "^\\d+:\\d+$"
205
+ },
206
+ "chromogen": {
207
+ "type": "string",
208
+ "title": "Chromogen",
209
+ "default": "DAB (brown)",
210
+ "enum": [
211
+ "DAB (brown)",
212
+ "AEC (red)",
213
+ "Fast Red (red)",
214
+ "NovaRED (red)",
215
+ "VIP (purple)",
216
+ "BCIP/NBT (blue)",
217
+ "Other"
218
+ ]
219
+ }
220
+ }
221
+ },
222
+ "aBeta": {
223
+ "type": "object",
224
+ "title": "Amyloid Beta",
225
+ "abbreviation": "Aβ",
226
+ "required": [
227
+ "antibody"
228
+ ],
229
+ "properties": {
230
+ "antibody": {
231
+ "type": "string",
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+ "title": "Antibody",
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+ "enum": [
234
+ "4G8",
235
+ "6E10"
236
+ ]
237
+ },
238
+ "vendor": {
239
+ "type": "string",
240
+ "title": "Vendor"
241
+ },
242
+ "dilution": {
243
+ "type": "string",
244
+ "title": "Dilution",
245
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
246
+ "pattern": "^\\d+:\\d+$"
247
+ },
248
+ "chromogen": {
249
+ "type": "string",
250
+ "title": "Chromogen",
251
+ "default": "DAB (brown)",
252
+ "enum": [
253
+ "DAB (brown)",
254
+ "AEC (red)",
255
+ "Fast Red (red)",
256
+ "NovaRED (red)",
257
+ "VIP (purple)",
258
+ "BCIP/NBT (blue)",
259
+ "Other"
260
+ ]
261
+ }
262
+ }
263
+ },
264
+ "LFB": {
265
+ "type": "object",
266
+ "title": "Luxol Fast Blue",
267
+ "abbreviation": "LFB",
268
+ "properties": {
269
+ "dilution": {
270
+ "type": "string",
271
+ "title": "Dilution",
272
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
273
+ "pattern": "^1:\\d+$",
274
+ "examples": [
275
+ "1:100",
276
+ "1:1000"
277
+ ]
278
+ },
279
+ "vendor": {
280
+ "type": "string",
281
+ "title": "Vendor"
282
+ }
283
+ }
284
+ },
285
+ "GFAP": {
286
+ "type": "object",
287
+ "title": "Glial Fibrillary Acidic Protein",
288
+ "abbreviation": "GFAP",
289
+ "properties": {
290
+ "dilution": {
291
+ "type": "string",
292
+ "title": "Dilution",
293
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
294
+ "pattern": "^1:\\d+$",
295
+ "examples": [
296
+ "1:100",
297
+ "1:1000"
298
+ ]
299
+ },
300
+ "vendor": {
301
+ "type": "string",
302
+ "title": "Vendor"
303
+ },
304
+ "chromogen": {
305
+ "type": "string",
306
+ "title": "Chromogen",
307
+ "default": "DAB (brown)",
308
+ "enum": [
309
+ "DAB (brown)",
310
+ "AEC (red)",
311
+ "Fast Red (red)",
312
+ "NovaRED (red)",
313
+ "VIP (purple)",
314
+ "BCIP/NBT (blue)",
315
+ "Other"
316
+ ]
317
+ }
318
+ }
319
+ },
320
+ "IBA1": {
321
+ "type": "object",
322
+ "title": "Ionized Calcium-Binding Adapter Molecule 1",
323
+ "abbreviation": "IBA1",
324
+ "properties": {
325
+ "dilution": {
326
+ "type": "string",
327
+ "title": "Dilution",
328
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
329
+ "pattern": "^1:\\d+$",
330
+ "examples": [
331
+ "1:100",
332
+ "1:1000"
333
+ ]
334
+ },
335
+ "vendor": {
336
+ "type": "string",
337
+ "title": "Vendor"
338
+ },
339
+ "chromogen": {
340
+ "type": "string",
341
+ "title": "Chromogen",
342
+ "default": "DAB (brown)",
343
+ "enum": [
344
+ "DAB (brown)",
345
+ "AEC (red)",
346
+ "Fast Red (red)",
347
+ "NovaRED (red)",
348
+ "VIP (purple)",
349
+ "BCIP/NBT (blue)",
350
+ "Other"
351
+ ]
352
+ }
353
+ }
354
+ },
355
+ "NeuN": {
356
+ "type": "object",
357
+ "title": "Neuronal Nuclei",
358
+ "abbreviation": "NeuN",
359
+ "properties": {
360
+ "dilution": {
361
+ "type": "string",
362
+ "title": "Dilution",
363
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
364
+ "pattern": "^1:\\d+$",
365
+ "examples": [
366
+ "1:100",
367
+ "1:1000"
368
+ ]
369
+ },
370
+ "vendor": {
371
+ "type": "string",
372
+ "title": "Vendor"
373
+ },
374
+ "chromogen": {
375
+ "type": "string",
376
+ "title": "Chromogen",
377
+ "default": "DAB (brown)",
378
+ "enum": [
379
+ "DAB (brown)",
380
+ "AEC (red)",
381
+ "Fast Red (red)",
382
+ "NovaRED (red)",
383
+ "VIP (purple)",
384
+ "BCIP/NBT (blue)",
385
+ "Other"
386
+ ]
387
+ }
388
+ }
389
+ },
390
+ "LFB-PAS": {
391
+ "type": "object",
392
+ "title": "Luxol Fast Blue - Periodic Acid-Schiff",
393
+ "abbreviation": "LFB-PAS",
394
+ "properties": {
395
+ "dilution": {
396
+ "type": "string",
397
+ "title": "Dilution",
398
+ "_comment": "Mapped to NCI CDE 'Laboratory Procedure Antibody Dilution Ratio Text' (CDE ID 2189728)",
399
+ "pattern": "^1:\\d+$",
400
+ "examples": [
401
+ "1:100",
402
+ "1:1000"
403
+ ]
404
+ },
405
+ "vendor": {
406
+ "type": "string",
407
+ "title": "Vendor"
408
+ }
409
+ }
410
+ }
411
+ },
412
+ "minProperties": 1,
413
+ "maxProperties": 1
414
+ },
415
+ "description": "List of stains used on the tissue section, each including the stain name and potentially additional information."
416
+ },
417
+ "regionIDs": {
418
+ "type": "object",
419
+ "title": "Region Information",
420
+ "required": [
421
+ "regions"
422
+ ],
423
+ "properties": {
424
+ "regions": {
425
+ "type": "object",
426
+ "title": "Regions",
427
+ "minItems": 1,
428
+ "additionalProperties": false,
429
+ "properties": {
430
+ "Olfactory Bulb": {
431
+ "type": "array",
432
+ "title": "Olfactory Bulb",
433
+ "abbreviation": "OB",
434
+ "items": {
435
+ "type": "string",
436
+ "enum": [
437
+ "Bulb",
438
+ "Tract"
439
+ ]
440
+ }
441
+ },
442
+ "Parietal Lobe": {
443
+ "type": "array",
444
+ "title": "Parietal Lobe",
445
+ "abbreviation": "Par",
446
+ "items": {
447
+ "type": "string",
448
+ "enum": [
449
+ "Super",
450
+ "Middle",
451
+ "Inferior",
452
+ "Angular gyrus",
453
+ "Supramarginal gyrus"
454
+ ]
455
+ }
456
+ },
457
+ "Temporal Pole": {
458
+ "type": "array",
459
+ "title": "Temporal Pole",
460
+ "abbreviation": "TempPole",
461
+ "items": {
462
+ "type": "string"
463
+ },
464
+ "maxItems": 0
465
+ },
466
+ "Frontal Lobe": {
467
+ "type": "array",
468
+ "title": "Frontal Lobe",
469
+ "abbreviation": "Frntl",
470
+ "items": {
471
+ "type": "string",
472
+ "enum": [
473
+ "Superior",
474
+ "Middle",
475
+ "Inferior"
476
+ ]
477
+ }
478
+ },
479
+ "Temporal Lobe": {
480
+ "type": "array",
481
+ "title": "Temporal Lobe",
482
+ "abbreviation": "Temp",
483
+ "items": {
484
+ "type": "string",
485
+ "enum": [
486
+ "Superior",
487
+ "Middle",
488
+ "Inferior"
489
+ ]
490
+ }
491
+ },
492
+ "Hippocampus": {
493
+ "type": "array",
494
+ "title": "Hippocampus",
495
+ "abbreviation": "Hipp",
496
+ "items": {
497
+ "type": "string",
498
+ "enum": [
499
+ "CA1-4 with dentate gyrus",
500
+ "Parahippocampal gyrus",
501
+ "Tail of caudate",
502
+ "Lateral geniculate nucleus",
503
+ "Occipital temporal gyrus"
504
+ ]
505
+ }
506
+ },
507
+ "Anterior Cingulate": {
508
+ "type": "array",
509
+ "title": "Anterior Cingulate",
510
+ "abbreviation": "ACg",
511
+ "items": {
512
+ "type": "string",
513
+ "enum": [
514
+ "Corpus callosum",
515
+ "Superior frontal"
516
+ ]
517
+ }
518
+ },
519
+ "Posterior Cingulate": {
520
+ "type": "array",
521
+ "title": "Posterior Cingulate",
522
+ "abbreviation": "PCg",
523
+ "items": {
524
+ "type": "string",
525
+ "enum": [
526
+ "Corpus callosum",
527
+ "Superior frontal"
528
+ ]
529
+ }
530
+ },
531
+ "Amygdala": {
532
+ "type": "array",
533
+ "title": "Amygdala",
534
+ "abbreviation": "Amyg",
535
+ "items": {
536
+ "type": "string",
537
+ "enum": [
538
+ "Entorhinal cortex"
539
+ ]
540
+ }
541
+ },
542
+ "Thalamus": {
543
+ "type": "array",
544
+ "title": "Thalamus",
545
+ "abbreviation": "Thal",
546
+ "items": {
547
+ "type": "string",
548
+ "enum": [
549
+ "Mammillary body",
550
+ "Subthalamic nucleus",
551
+ "Mammilo-thalmaic tract",
552
+ "Anterior nucleus of thalamus",
553
+ "Pulvinar"
554
+ ]
555
+ }
556
+ },
557
+ "White Matter": {
558
+ "type": "array",
559
+ "title": "White Matter",
560
+ "abbreviation": "WM",
561
+ "items": {
562
+ "type": "string",
563
+ "enum": [
564
+ "Frontal",
565
+ "Parietal",
566
+ "Temporal",
567
+ "Occipital"
568
+ ]
569
+ }
570
+ },
571
+ "Midbrain": {
572
+ "type": "array",
573
+ "title": "Midbrain",
574
+ "abbreviation": "MidBrn",
575
+ "items": {
576
+ "type": "string",
577
+ "enum": [
578
+ "3rd cranial nerve",
579
+ "Substantia nigra",
580
+ "Red nucleus",
581
+ "Superior colliculus"
582
+ ]
583
+ }
584
+ },
585
+ "Pons": {
586
+ "type": "array",
587
+ "title": "Pons",
588
+ "abbreviation": "Pons",
589
+ "items": {
590
+ "type": "string",
591
+ "enum": [
592
+ "Superior cerebellar peduncle",
593
+ "Inferior colliculus",
594
+ "Locus coeruleus",
595
+ "Pontine base / fibers"
596
+ ]
597
+ }
598
+ },
599
+ "Medulla": {
600
+ "type": "array",
601
+ "title": "Medulla",
602
+ "abbreviation": "Med",
603
+ "items": {
604
+ "type": "string",
605
+ "enum": [
606
+ "Dorsal motor nucleus of vagus",
607
+ "Hypoglossal nucleus",
608
+ "Inferior olive",
609
+ "Medullary velum",
610
+ "Pyramid"
611
+ ]
612
+ }
613
+ },
614
+ "Cerebellum": {
615
+ "type": "array",
616
+ "title": "Cerebellum",
617
+ "abbreviation": "Cblm",
618
+ "items": {
619
+ "type": "string",
620
+ "enum": [
621
+ "Dentate",
622
+ "Vermis",
623
+ "Cortex"
624
+ ]
625
+ }
626
+ },
627
+ "Basal Ganglia": {
628
+ "type": "array",
629
+ "title": "Basal Ganglia",
630
+ "abbreviation": "BG",
631
+ "items": {
632
+ "type": "string"
633
+ },
634
+ "maxItems": 0
635
+ },
636
+ "Occipital Lobe": {
637
+ "type": "array",
638
+ "title": "Occipital Lobe",
639
+ "abbreviation": "Occ",
640
+ "items": {
641
+ "type": "string"
642
+ },
643
+ "maxItems": 0
644
+ },
645
+ "Primary Motor Cortex": {
646
+ "type": "array",
647
+ "title": "Primary Motor Cortex",
648
+ "abbreviation": "M1",
649
+ "items": {
650
+ "type": "string"
651
+ },
652
+ "maxItems": 0
653
+ },
654
+ "Insula": {
655
+ "type": "array",
656
+ "title": "Insula",
657
+ "abbreviation": "Ins",
658
+ "items": {
659
+ "type": "string"
660
+ },
661
+ "maxItems": 0
662
+ },
663
+ "Frontal Pole": {
664
+ "type": "array",
665
+ "title": "Frontal Pole",
666
+ "abbreviation": "FtlPole",
667
+ "items": {
668
+ "type": "string"
669
+ },
670
+ "maxItems": 0
671
+ },
672
+ "Spinal Cord": {
673
+ "type": "array",
674
+ "title": "Spinal Cord",
675
+ "abbreviation": "SpnCd",
676
+ "items": {
677
+ "type": "string",
678
+ "enum": [
679
+ "Lower",
680
+ "Middle",
681
+ "Upper"
682
+ ]
683
+ }
684
+ },
685
+ "Hypothalamus": {
686
+ "type": "array",
687
+ "title": "Hypothalamus",
688
+ "abbreviation": "Hyp",
689
+ "items": {
690
+ "type": "string"
691
+ },
692
+ "maxItems": 0
693
+ }
694
+ }
695
+ },
696
+ "hemisphere": {
697
+ "type": "string",
698
+ "title": "Hemisphere",
699
+ "enum": [
700
+ "left",
701
+ "right"
702
+ ]
703
+ },
704
+ "sliceOrientation": {
705
+ "title": "Slice Orientation",
706
+ "type": "string",
707
+ "enum": [
708
+ "axial",
709
+ "coronal",
710
+ "sagittal"
711
+ ]
712
+ },
713
+ "damage": {
714
+ "type": "array",
715
+ "title": "Damage",
716
+ "description": "Specifies tissue damage in this region and the cause of it.",
717
+ "items": {
718
+ "type": "string",
719
+ "enum": [
720
+ "Infarct",
721
+ "Lacune",
722
+ "Microinfarct",
723
+ "CTE",
724
+ "TBI"
725
+ ]
726
+ }
727
+ },
728
+ "sliceThickness": {
729
+ "type": "number",
730
+ "title": "Slice Thickness",
731
+ "description": "Thickness of the tissue slice in microns (μm). This represents the physical thickness of the tissue section.",
732
+ "minimum": 0.1,
733
+ "maximum": 1000,
734
+ "multipleOf": 0.1
735
+ },
736
+ "landmarks": {
737
+ "type": "array",
738
+ "title": "Landmarks",
739
+ "description": "Multiple anatomical landmarks present in this region (allows for non-mutually exclusive landmarks)",
740
+ "items": {
741
+ "type": "string"
742
+ },
743
+ "uniqueItems": true
744
+ }
745
+ }
746
+ },
747
+ "slideComments": {
748
+ "type": "string",
749
+ "description": "Optional free text field for additional comments about the slide."
750
+ },
751
+ "slideIndex": {
752
+ "type": "integer",
753
+ "default": 1,
754
+ "description": "Index of the slide when multiple sections have the same stain and block information, or if there are replicates."
755
+ },
756
+ "otherCaseIdentifiers": {
757
+ "type": "array",
758
+ "items": {
759
+ "type": "object",
760
+ "properties": {
761
+ "caseID": {
762
+ "type": "string",
763
+ "description": "Other unique identifier for the case from other repositires."
764
+ },
765
+ "caseSource": {
766
+ "type": "string",
767
+ "description": "The source of the case identifier, e.g., NACC, NIGAD, dbGAP, ADNI.",
768
+ "enum": [
769
+ "NACC",
770
+ "NIGAD",
771
+ "dbGAP",
772
+ "ADNI"
773
+ ]
774
+ }
775
+ },
776
+ "required": [
777
+ "caseID",
778
+ "caseSource"
779
+ ],
780
+ "description": "An object containing both the caseID and the caseSource for other case identifiers associated with the case."
781
+ },
782
+ "description": "List of other case identifiers that may be associated with the case, each including a caseID and a caseSource."
783
+ },
784
+ "clinicalData": {
785
+ "type": "object",
786
+ "title": "Clinical Metadata",
787
+ "description": "The metadata fields that each case must have to include in the BDSA database, based on NACC fields.",
788
+ "required": [
789
+ "NPSEX",
790
+ "NACCDAGE",
791
+ "EDUC",
792
+ "HISPANIC",
793
+ "NACCUDSD",
794
+ "RACE",
795
+ "NPPMIH",
796
+ "NPADNC"
797
+ ],
798
+ "properties": {
799
+ "NACCID": {
800
+ "type": "string",
801
+ "title": "NACC ID",
802
+ "description": "NACCID is a unique identifier for each case in the NACC database."
803
+ },
804
+ "NPSEX": {
805
+ "type": "integer",
806
+ "title": "Sex",
807
+ "enum": [
808
+ 1,
809
+ 2
810
+ ],
811
+ "description": "1=male, 2=female. NACC variable.\nCDE: `sex`",
812
+ "cde": "sex"
813
+ },
814
+ "NACCDAGE": {
815
+ "type": "integer",
816
+ "title": "Age at Death",
817
+ "description": "Age at death in years. NACC variable.\nCDE: `age_at_death`",
818
+ "cde": "age_at_death"
819
+ },
820
+ "EDUC": {
821
+ "type": "integer",
822
+ "title": "Years of Education",
823
+ "description": "Number of years of formal education. NACC variable.\nCDE: `years_of_education`",
824
+ "cde": "years_of_education"
825
+ },
826
+ "HISPANIC": {
827
+ "type": "integer",
828
+ "title": "Hispanic Ethnicity",
829
+ "enum": [
830
+ 0,
831
+ 1
832
+ ],
833
+ "description": "0=no, 1=yes. NACC variable.\nCDE: `hispanic_ethnicity`",
834
+ "cde": "hispanic_ethnicity"
835
+ },
836
+ "NACCUDSD": {
837
+ "type": "integer",
838
+ "title": "NACC UDS Dementia Status",
839
+ "enum": [
840
+ 1,
841
+ 2,
842
+ 3,
843
+ 4,
844
+ 5,
845
+ 6,
846
+ 7,
847
+ 8,
848
+ 9
849
+ ],
850
+ "description": "NACC UDS Dementia Status. NACC variable.\nCDE: `dementia_status`",
851
+ "cde": "dementia_status"
852
+ },
853
+ "RACE": {
854
+ "type": "integer",
855
+ "title": "Race",
856
+ "enum": [
857
+ 1,
858
+ 2,
859
+ 3,
860
+ 4,
861
+ 5,
862
+ 6,
863
+ 7,
864
+ 8,
865
+ 9
866
+ ],
867
+ "description": "Race categories. NACC variable.\nCDE: `race`",
868
+ "cde": "race"
869
+ },
870
+ "NPPMIH": {
871
+ "type": "integer",
872
+ "title": "NACC PMI Hours",
873
+ "description": "Post-mortem interval in hours. NACC variable.\nCDE: `pmi_hours`",
874
+ "cde": "pmi_hours"
875
+ },
876
+ "NPADNC": {
877
+ "type": "integer",
878
+ "title": "NACC ADNC",
879
+ "enum": [
880
+ 1,
881
+ 2,
882
+ 3,
883
+ 4,
884
+ 5,
885
+ 6,
886
+ 7,
887
+ 8,
888
+ 9
889
+ ],
890
+ "description": "NACC ADNC (Alzheimer's Disease Neuropathologic Change) score. NACC variable.\nCDE: `adnc_score`",
891
+ "cde": "adnc_score"
892
+ }
893
+ }
894
+ }
895
+ }
896
+ }