diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a7c194bd2..13133dcd3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,7 +22,7 @@ repos: rev: v2.4.1 hooks: - id: codespell - exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml)$ + exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml|dandi/data/allen_ccf_structures\.json)$ additional_dependencies: - tomli; python_version<'3.11' - repo: https://github.com/PyCQA/flake8 diff --git a/dandi/data/__init__.py b/dandi/data/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/dandi/data/allen_ccf_structures.json b/dandi/data/allen_ccf_structures.json new file mode 100644 index 000000000..e31ecda2d --- /dev/null +++ b/dandi/data/allen_ccf_structures.json @@ -0,0 +1 @@ +[{"id":1,"acronym":"TMv","name":"Tuberomammillary nucleus, ventral part"},{"id":2,"acronym":"SSp-m6b","name":"Primary somatosensory area, mouth, layer 6b"},{"id":3,"acronym":"sec","name":"secondary fissure"},{"id":4,"acronym":"IC","name":"Inferior colliculus"},{"id":6,"acronym":"int","name":"internal capsule"},{"id":7,"acronym":"PSV","name":"Principal sensory nucleus of the trigeminal"},{"id":8,"acronym":"grey","name":"Basic cell groups and regions"},{"id":9,"acronym":"SSp-tr6a","name":"Primary somatosensory area, trunk, layer 6a"},{"id":10,"acronym":"SCig","name":"Superior colliculus, motor related, intermediate gray layer"},{"id":11,"acronym":"plf","name":"posterolateral fissure"},{"id":12,"acronym":"IF","name":"Interfascicular nucleus raphe"},{"id":14,"acronym":"im","name":"internal medullary lamina of the thalamus"},{"id":15,"acronym":"PT","name":"Parataenial nucleus"},{"id":16,"acronym":"6b","name":"Layer 6b, isocortex"},{"id":17,"acronym":"SCiw","name":"Superior colliculus, motor related, intermediate white layer"},{"id":18,"acronym":"nf","name":"nodular fissure"},{"id":19,"acronym":"IG","name":"Induseum 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2/3"},{"id":305,"acronym":"VISp6b","name":"Primary visual area, layer 6b"},{"id":306,"acronym":"TTv1-3","name":"Taenia tecta, ventral part, layers 1-3"},{"id":307,"acronym":"MARN","name":"Magnocellular reticular nucleus"},{"id":308,"acronym":"PTLp6a","name":"Posterior parietal association areas, layer 6a"},{"id":309,"acronym":"snp","name":"striatonigral pathway"},{"id":310,"acronym":"SF","name":"Septofimbrial nucleus"},{"id":311,"acronym":"BLAp","name":"Basolateral amygdalar nucleus, posterior part"},{"id":312,"acronym":"ENTl4/5","name":"Entorhinal area, lateral part, layer 4/5"},{"id":313,"acronym":"MB","name":"Midbrain"},{"id":314,"acronym":"AIp6a","name":"Agranular insular area, posterior part, layer 6a"},{"id":315,"acronym":"Isocortex","name":"Isocortex"},{"id":316,"acronym":"LGvm","name":"Ventral part of the lateral geniculate complex, medial zone"},{"id":317,"acronym":"stf","name":"subthalamic fascicle"},{"id":318,"acronym":"SG","name":"Supragenual nucleus"},{"id":319,"acronym":"BMA","name":"Basomedial amygdalar nucleus"},{"id":320,"acronym":"MOp1","name":"Primary motor area, Layer 1"},{"id":321,"acronym":"SubG","name":"Subgeniculate nucleus"},{"id":322,"acronym":"SSp","name":"Primary somatosensory area"},{"id":323,"acronym":"MBmot","name":"Midbrain, motor related"},{"id":324,"acronym":"ENTmv2","name":"Entorhinal area, medial part, ventral zone, layer 2"},{"id":325,"acronym":"SGN","name":"Suprageniculate nucleus"},{"id":326,"acronym":"scp","name":"superior cerebelar peduncles"},{"id":327,"acronym":"BMAa","name":"Basomedial amygdalar nucleus, anterior part"},{"id":328,"acronym":"AId2/3","name":"Agranular insular area, dorsal part, layer 2/3"},{"id":329,"acronym":"SSp-bfd","name":"Primary somatosensory area, barrel field"},{"id":330,"acronym":"RSPd6b","name":"Retrosplenial area, dorsal part, layer 6b"},{"id":331,"acronym":"MBO","name":"Mammillary body"},{"id":332,"acronym":"ASO","name":"Accessory supraoptic group"},{"id":333,"acronym":"SH","name":"Septohippocampal nucleus"},{"id":334,"acronym":"BMAp","name":"Basomedial amygdalar nucleus, posterior part"},{"id":335,"acronym":"PERI6a","name":"Perirhinal area, layer 6a"},{"id":336,"acronym":"csc","name":"superior colliculus commissure"},{"id":337,"acronym":"SSp-ll","name":"Primary somatosensory area, lower limb"},{"id":338,"acronym":"SFO","name":"Subfornical organ"},{"id":339,"acronym":"MBsen","name":"Midbrain, sensory related"},{"id":340,"acronym":"PTLp6b","name":"Posterior parietal association areas, layer 6b"},{"id":341,"acronym":"smd","name":"supramammillary decussation"},{"id":342,"acronym":"SI","name":"Substantia innominata"},{"id":343,"acronym":"BS","name":"Brain stem"},{"id":344,"acronym":"AIp5","name":"Agranular insular area, posterior part, layer 5"},{"id":345,"acronym":"SSp-m","name":"Primary somatosensory area, mouth"},{"id":346,"acronym":"SSp2/3","name":"Primary somatosensory area, layer 2/3"},{"id":347,"acronym":"SBPV","name":"Subparaventricular zone"},{"id":348,"acronym":"MBsta","name":"Midbrain, behavioral state related"},{"id":349,"acronym":"sup","name":"supraoptic commissures"},{"id":350,"acronym":"SLC","name":"Subceruleus nucleus"},{"id":351,"acronym":"BST","name":"Bed nuclei of the stria terminalis"},{"id":352,"acronym":"ORB5","name":"Orbital area, layer 5"},{"id":353,"acronym":"SSp-n","name":"Primary somatosensory area, nose"},{"id":354,"acronym":"MY","name":"Medulla"},{"id":355,"acronym":"AIp6b","name":"Agranular insular area, posterior part, layer 6b"},{"id":356,"acronym":"PST","name":"Preparasubthalamic nucleus"},{"id":357,"acronym":"ttp","name":"tectothalamic pathway"},{"id":358,"acronym":"SLD","name":"Sublaterodorsal nucleus"},{"id":359,"acronym":"BSTa","name":"Bed nuclei of the stria terminalis, anterior division"},{"id":360,"acronym":"DP2/3","name":"Dorsal peduncular area, layer 2/3"},{"id":361,"acronym":"SSp-tr","name":"Primary somatosensory area, trunk"},{"id":362,"acronym":"MD","name":"Mediodorsal nucleus of thalamus"},{"id":363,"acronym":"PL5","name":"Prelimbic area, layer 5"},{"id":364,"acronym":"PSTN","name":"Parasubthalamic nucleus"},{"id":365,"acronym":"tp","name":"thalamic peduncles"},{"id":366,"acronym":"SMT","name":"Submedial nucleus of the thalamus"},{"id":367,"acronym":"BSTp","name":"Bed nuclei of the stria terminalis, posterior division"},{"id":368,"acronym":"PERI6b","name":"Perirhinal area, layer 6b"},{"id":369,"acronym":"SSp-ul","name":"Primary somatosensory area, upper limb"},{"id":370,"acronym":"MY-mot","name":"Medulla, motor related"},{"id":371,"acronym":"ENTmv3","name":"Entorhinal area, medial part, ventral zone, layer 3"},{"id":372,"acronym":"ICB","name":"Infracerebellar nucleus"},{"id":373,"acronym":"tct","name":"trigeminocerebellar tract"},{"id":374,"acronym":"SNc","name":"Substantia nigra, compact part"},{"id":375,"acronym":"CA","name":"Ammon's horn"},{"id":376,"acronym":"COApl1-3","name":"Cortical amygdalar area, posterior part, lateral zone, layers 1-3"},{"id":377,"acronym":"VISpl6a","name":"Posterolateral visual area, layer 6a"},{"id":378,"acronym":"SSs","name":"Supplemental somatosensory area"},{"id":379,"acronym":"MY-sat","name":"Medulla, behavioral state related"},{"id":380,"acronym":"cuf","name":"cuneate fascicle"},{"id":381,"acronym":"SNr","name":"Substantia nigra, reticular part"},{"id":382,"acronym":"CA1","name":"Field CA1"},{"id":383,"acronym":"COApm1-3","name":"Cortical amygdalar area, posterior part, medial zone, layers 1-3"},{"id":384,"acronym":"IVd","name":"trochlear nerve decussation"},{"id":385,"acronym":"VISp","name":"Primary visual area"},{"id":386,"acronym":"MY-sen","name":"Medulla, sensory related"},{"id":387,"acronym":"ENTl5/6","name":"Entorhinal area, lateral part, layer 5/6"},{"id":388,"acronym":"grf","name":"gracile fascicle"},{"id":389,"acronym":"sttv","name":"ventral spinothalamic tract"},{"id":390,"acronym":"SO","name":"Supraoptic nucleus"},{"id":391,"acronym":"CA1slm","name":"Field CA1, stratum lacunosum-moleculare"},{"id":392,"acronym":"NLOT1-3","name":"Nucleus of the lateral olfactory tract, layers 1-3"},{"id":393,"acronym":"VISpl6b","name":"Posterolateral visual area, layer 6b"},{"id":394,"acronym":"VISam","name":"Anteromedial visual area"},{"id":395,"acronym":"MDRN","name":"Medullary reticular nucleus"},{"id":396,"acronym":"iaf","name":"internal arcuate fibers"},{"id":397,"acronym":"vtd","name":"ventral tegmental decussation"},{"id":398,"acronym":"SOC","name":"Superior olivary complex"},{"id":399,"acronym":"CA1so","name":"Field CA1, stratum oriens"},{"id":400,"acronym":"PAA1-3","name":"Piriform-amygdalar area, layers 1-3"},{"id":401,"acronym":"VISam4","name":"Anteromedial visual area, layer 4"},{"id":402,"acronym":"VISal","name":"Anterolateral visual area"},{"id":403,"acronym":"MEA","name":"Medial amygdalar nucleus"},{"id":404,"acronym":"oct","name":"olivocerebellar tract"},{"id":405,"acronym":"vlt","name":"ventrolateral hypothalamic tract"},{"id":406,"acronym":"SPF","name":"Subparafascicular nucleus"},{"id":407,"acronym":"CA1sp","name":"Field CA1, pyramidal layer"},{"id":408,"acronym":"PAA1","name":"Piriform-amygdalar area, molecular layer"},{"id":409,"acronym":"VISl","name":"Lateral visual area"},{"id":410,"acronym":"rct","name":"reticulocerebellar tract"},{"id":411,"acronym":"MEAad","name":"Medial amygdalar nucleus, anterodorsal part"},{"id":412,"acronym":"ORBl2/3","name":"Orbital area, lateral part, layer 2/3"},{"id":413,"acronym":"vVIIIn","name":"vestibular nerve"},{"id":414,"acronym":"SPFm","name":"Subparafascicular nucleus, magnocellular part"},{"id":415,"acronym":"CA1sr","name":"Field CA1, stratum radiatum"},{"id":416,"acronym":"PAA2","name":"Piriform-amygdalar area, pyramidal layer"},{"id":417,"acronym":"VISrl","name":"Rostrolateral visual area"},{"id":418,"acronym":"MEAav","name":"Medial amygdalar nucleus, anteroventral part"},{"id":419,"acronym":"ENTmv4","name":"Entorhinal area, medial part, ventral zone, layer 4"},{"id":420,"acronym":"db","name":"precommissural fornix diagonal band"},{"id":421,"acronym":"VISl1","name":"Lateral visual area, layer 1"},{"id":422,"acronym":"SPFp","name":"Subparafascicular nucleus, parvicellular part"},{"id":423,"acronym":"CA2","name":"Field CA2"},{"id":424,"acronym":"PAA3","name":"Piriform-amygdalar area, polymorph layer"},{"id":425,"acronym":"VISpl","name":"Posterolateral visual area"},{"id":426,"acronym":"MEApd","name":"Medial amygdalar nucleus, posterodorsal part"},{"id":427,"acronym":"ECT2/3","name":"Ectorhinal area/Layer 2/3"},{"id":428,"acronym":"mct","name":"medial corticohypothalamic tract"},{"id":429,"acronym":"SPVC","name":"Spinal nucleus of the trigeminal, caudal part"},{"id":430,"acronym":"RSPv2/3","name":"Retrosplenial area, ventral part, layer 2/3"},{"id":431,"acronym":"CA2slm","name":"Field CA2, stratum lacunosum-moleculare"},{"id":432,"acronym":"NC","name":"Nucleus circularis"},{"id":433,"acronym":"VISam5","name":"Anteromedial visual area, layer 5"},{"id":434,"acronym":"RSPd2/3","name":"Retrosplenial area, dorsal part, layer 2/3"},{"id":435,"acronym":"MEApv","name":"Medial amygdalar nucleus, posteroventral part"},{"id":436,"acronym":"fx","name":"columns of the fornix"},{"id":437,"acronym":"SPVI","name":"Spinal nucleus of the trigeminal, interpolar part"},{"id":438,"acronym":"CA2so","name":"Field CA2, stratum oriens"},{"id":439,"acronym":"PVHdp","name":"Paraventricular hypothalamic nucleus, descending division, dorsal parvicellular part"},{"id":440,"acronym":"ORBl6a","name":"Orbital area, lateral part, layer 6a"},{"id":441,"acronym":"VISam6b","name":"Anteromedial visual area, layer 6b"},{"id":442,"acronym":"RSPd1","name":"Retrosplenial area, dorsal part, layer 1"},{"id":443,"acronym":"dhc","name":"dorsal hippocampal commissure"},{"id":444,"acronym":"MED","name":"Medial group of the dorsal thalamus"},{"id":445,"acronym":"SPVO","name":"Spinal nucleus of the trigeminal, oral part"},{"id":446,"acronym":"CA2sp","name":"Field CA2, pyramidal layer"},{"id":447,"acronym":"PVHf","name":"Paraventricular hypothalamic nucleus, descending division, forniceal part"},{"id":448,"acronym":"ORBl1","name":"Orbital area, lateral part, layer 1"},{"id":449,"acronym":"vhc","name":"ventral hippocampal commissure"},{"id":450,"acronym":"SSp-ul1","name":"Primary somatosensory area, upper limb, layer 1"},{"id":451,"acronym":"BLAv","name":"Basolateral amygdalar nucleus, ventral part"},{"id":452,"acronym":"MEPO","name":"Median preoptic nucleus"},{"id":453,"acronym":"SS","name":"Somatosensory areas"},{"id":454,"acronym":"CA2sr","name":"Field CA2, stratum radiatum"},{"id":455,"acronym":"PVHlp","name":"Paraventricular hypothalamic nucleus, descending division, lateral parvicellular part"},{"id":456,"acronym":"AUDpo6b","name":"Posterior auditory area, layer 6b"},{"id":457,"acronym":"VIS6a","name":"Visual areas, layer 6a"},{"id":458,"acronym":"OT1","name":"Olfactory tubercle, molecular layer"},{"id":459,"acronym":"aolt","name":"accessory olfactory tract"},{"id":460,"acronym":"MEV","name":"Midbrain trigeminal nucleus"},{"id":461,"acronym":"SSp-tr6b","name":"Primary somatosensory area, trunk, layer 6b"},{"id":462,"acronym":"SSN","name":"Superior salivatory nucleus"},{"id":463,"acronym":"CA3","name":"Field CA3"},{"id":464,"acronym":"PVHmpv","name":"Paraventricular hypothalamic nucleus, descending division, medial parvicellular part, ventral zone"},{"id":465,"acronym":"OT2","name":"Olfactory tubercle, pyramidal layer"},{"id":466,"acronym":"alv","name":"alveus"},{"id":467,"acronym":"MEZ","name":"Hypothalamic medial zone"},{"id":468,"acronym":"ENTm2a","name":"Entorhinal area, medial part, dorsal zone, layer 2a"},{"id":469,"acronym":"VISpm6b","name":"posteromedial visual area, layer 6b"},{"id":470,"acronym":"STN","name":"Subthalamic nucleus"},{"id":471,"acronym":"CA3slm","name":"Field CA3, stratum lacunosum-moleculare"},{"id":472,"acronym":"MEApd-a","name":"Medial amygdalar nucleus, posterodorsal part, sublayer a"},{"id":473,"acronym":"OT3","name":"Olfactory tubercle, polymorph layer"},{"id":474,"acronym":"ab","name":"angular path"},{"id":475,"acronym":"MG","name":"Medial geniculate complex"},{"id":476,"acronym":"ORB6a","name":"Orbital area, layer 6a"},{"id":477,"acronym":"STR","name":"Striatum"},{"id":478,"acronym":"SSp-ll6a","name":"Primary somatosensory area, lower limb, layer 6a"},{"id":479,"acronym":"CA3slu","name":"Field CA3, stratum lucidum"},{"id":480,"acronym":"MEApd-b","name":"Medial amygdalar nucleus, posterodorsal part, sublayer b"},{"id":481,"acronym":"isl","name":"Islands of Calleja"},{"id":482,"acronym":"bic","name":"brachium of the inferior colliculus"},{"id":483,"acronym":"MH","name":"Medial habenula"},{"id":484,"acronym":"ORBm1","name":"Orbital area, medial part, layer 1"},{"id":485,"acronym":"STRd","name":"Striatum dorsal region"},{"id":486,"acronym":"CA3so","name":"Field CA3, stratum oriens"},{"id":487,"acronym":"MEApd-c","name":"Medial amygdalar nucleus, posterodorsal part, sublayer c"},{"id":488,"acronym":"ORBl6b","name":"Orbital area, lateral part, layer 6b"},{"id":489,"acronym":"islm","name":"Major island of Calleja"},{"id":490,"acronym":"bct","name":"bulbocerebellar tract"},{"id":491,"acronym":"MM","name":"Medial mammillary nucleus"},{"id":492,"acronym":"ORB2/3","name":"Orbital area, layer 2/3"},{"id":493,"acronym":"STRv","name":"Striatum ventral region"},{"id":494,"acronym":"SCig-a","name":"Superior colliculus, motor related, intermediate gray layer, sublayer a"},{"id":495,"acronym":"CA3sp","name":"Field CA3, pyramidal layer"},{"id":496,"acronym":"DP1","name":"Dorsal peduncular area, layer 1"},{"id":497,"acronym":"VIS6b","name":"Visual areas, layer 6b"},{"id":498,"acronym":"BSTam","name":"Bed nuclei of the stria terminalis, anterior division, anteromedial area"},{"id":499,"acronym":"cct","name":"cuneocerebellar tract"},{"id":500,"acronym":"MO","name":"Somatomotor areas"},{"id":501,"acronym":"VISpm4","name":"posteromedial visual area, layer 4"},{"id":502,"acronym":"SUB","name":"Subiculum"},{"id":503,"acronym":"SCig-b","name":"Superior colliculus, motor related, intermediate gray layer, sublayer b"},{"id":504,"acronym":"CA3sr","name":"Field CA3, stratum radiatum"},{"id":505,"acronym":"BSTdm","name":"Bed nuclei of the stria terminalis, anterior division, dorsomedial nucleus"},{"id":506,"acronym":"das","name":"dorsal acoustic stria"},{"id":507,"acronym":"MOB","name":"Main olfactory bulb"},{"id":508,"acronym":"ENTm2b","name":"Entorhinal area, medial part, dorsal zone, layer 2b"},{"id":509,"acronym":"SUBd","name":"Subiculum, dorsal part"},{"id":510,"acronym":"SSp-ll6b","name":"Primary somatosensory area, lower limb, layer 6b"},{"id":511,"acronym":"SCig-c","name":"Superior colliculus, motor related, intermediate gray layer, sublayer c"},{"id":512,"acronym":"CB","name":"Cerebellum"},{"id":513,"acronym":"BSTfu","name":"Bed nuclei of the stria terminalis, anterior division, fusiform nucleus"},{"id":514,"acronym":"dc","name":"dorsal column"},{"id":515,"acronym":"MPN","name":"Medial preoptic nucleus"},{"id":516,"acronym":"ORB6b","name":"Orbital area, layer 6b"},{"id":517,"acronym":"TR1-3","name":"Postpiriform transition area, layers 1-3"},{"id":518,"acronym":"SUBv","name":"Subiculum, ventral part"},{"id":519,"acronym":"CBN","name":"Cerebellar nuclei"},{"id":520,"acronym":"AUDv6a","name":"Ventral auditory area, layer 6a"},{"id":521,"acronym":"BSTmg","name":"Bed nuclei of the stria terminalis, anterior division, magnocellular nucleus"},{"id":522,"acronym":"dcm","name":"dorsal commissure of the spinal cord"},{"id":523,"acronym":"MPO","name":"Medial preoptic area"},{"id":524,"acronym":"ORBm2","name":"Orbital area, medial part, layer 2"},{"id":525,"acronym":"SUM","name":"Supramammillary nucleus"},{"id":526,"acronym":"ENTm1","name":"Entorhinal area, medial part, dorsal zone, layer 1"},{"id":527,"acronym":"AUDd1","name":"Dorsal auditory area, layer 1"},{"id":528,"acronym":"CBX","name":"Cerebellar cortex"},{"id":529,"acronym":"BSTv","name":"Bed nuclei of the stria terminalis, anterior division, ventral nucleus"},{"id":530,"acronym":"df","name":"dorsal fornix"},{"id":531,"acronym":"MPT","name":"Medial pretectal area"},{"id":532,"acronym":"PTLp1","name":"Posterior parietal association areas, layer 1"},{"id":533,"acronym":"VISpm","name":"posteromedial visual area"},{"id":534,"acronym":"SUT","name":"Supratrigeminal nucleus"},{"id":535,"acronym":"DP2","name":"Dorsal peduncular area, layer 2"},{"id":536,"acronym":"CEA","name":"Central amygdalar nucleus"},{"id":537,"acronym":"BSTal","name":"Bed nuclei of the stria terminalis, anterior division, anterolateral area"},{"id":538,"acronym":"lotd","name":"dorsal limb"},{"id":539,"acronym":"MRNm","name":"Midbrain reticular nucleus, magnocellular part"},{"id":540,"acronym":"PERI1","name":"Perirhinal area, layer 1"},{"id":541,"acronym":"TEa","name":"Temporal association areas"},{"id":542,"acronym":"RSPv1","name":"Retrosplenial area, ventral part, layer 1"},{"id":543,"acronym":"ENTm2","name":"Entorhinal area, medial part, dorsal zone, layer 2"},{"id":544,"acronym":"CEAc","name":"Central amygdalar nucleus, capsular part"},{"id":545,"acronym":"RSPd4","name":"Retrosplenial area, dorsal part, layer 4"},{"id":546,"acronym":"BSTju","name":"Bed nuclei of the stria terminalis, anterior division, juxtacapsular nucleus"},{"id":547,"acronym":"dlf","name":"dorsal longitudinal fascicle"},{"id":548,"acronym":"MRNmg","name":"Midbrain reticular nucleus, magnocellular part, general"},{"id":549,"acronym":"TH","name":"Thalamus"},{"id":550,"acronym":"ENTm5/6","name":"Entorhinal area, medial part, dorsal zone, layer 5/6"},{"id":551,"acronym":"CEAl","name":"Central amygdalar nucleus, lateral part"},{"id":552,"acronym":"PRNv","name":"Pontine reticular nucleus, ventral part"},{"id":553,"acronym":"sctd","name":"dorsal spinocerebellar tract"},{"id":554,"acronym":"BSTov","name":"Bed nuclei of the stria terminalis, anterior division, oval nucleus"},{"id":555,"acronym":"MRNp","name":"Midbrain reticular nucleus, parvicellular part"},{"id":556,"acronym":"ILA2/3","name":"Infralimbic area, layer 2/3"},{"id":557,"acronym":"TM","name":"Tuberomammillary nucleus"},{"id":558,"acronym":"SSp-n1","name":"Primary somatosensory area, nose, layer 1"},{"id":559,"acronym":"CEAm","name":"Central amygdalar nucleus, medial part"},{"id":560,"acronym":"CNspg","name":"Cochlear nucleus, subpedunclular granular region"},{"id":561,"acronym":"VIS2/3","name":"Visual areas, layer 2/3"},{"id":562,"acronym":"BSTrh","name":"Bed nuclei of the stria terminalis, anterior division, rhomboid nucleus"},{"id":563,"acronym":"dtt","name":"dorsal tegmental tract"},{"id":564,"acronym":"MS","name":"Medial septal nucleus"},{"id":565,"acronym":"VISpm5","name":"posteromedial visual area, layer 5"},{"id":566,"acronym":"TR","name":"Postpiriform transition area"},{"id":567,"acronym":"CH","name":"Cerebrum"},{"id":568,"acronym":"ACVI","name":"Accessory abducens nucleus"},{"id":569,"acronym":"BSTd","name":"Bed nuclei of the stria terminalis, posterior division, dorsal nucleus"},{"id":570,"acronym":"dl","name":"dorsolateral fascicle"},{"id":571,"acronym":"MTN","name":"Midline group of the dorsal thalamus"},{"id":572,"acronym":"ACA1","name":"Anterior cingulate area, layer 1"},{"id":573,"acronym":"VISl4","name":"Lateral visual area, layer 4"},{"id":574,"acronym":"TRN","name":"Tegmental reticular nucleus"},{"id":575,"acronym":"CL","name":"Central lateral nucleus of the thalamus"},{"id":576,"acronym":"ACVII","name":"Accessory facial motor nucleus"},{"id":577,"acronym":"SSp-ul4","name":"Primary somatosensory area, upper limb, layer 4"},{"id":578,"acronym":"BSTpr","name":"Bed nuclei of the stria terminalis, posterior division, principal nucleus"},{"id":579,"acronym":"ec","name":"external capsule"},{"id":580,"acronym":"NB","name":"Nucleus of the brachium of the inferior colliculus"},{"id":581,"acronym":"TRS","name":"Triangular nucleus of septum"},{"id":582,"acronym":"ORBm2/3","name":"Orbital area, medial part, layer 2/3"},{"id":583,"acronym":"CLA","name":"Claustrum"},{"id":584,"acronym":"COApl1-2","name":"Cortical amygdalar area, posterior part, lateral zone, layers 1-2"},{"id":585,"acronym":"BSTif","name":"Bed nuclei of the stria terminalis, posterior division, interfascicular nucleus"},{"id":586,"acronym":"fpr","name":"fasciculus proprius"},{"id":587,"acronym":"ND","name":"Nucleus of Darkschewitsch"},{"id":588,"acronym":"ACAv1","name":"Anterior cingulate area, ventral part, layer 1"},{"id":589,"acronym":"TT","name":"Taenia tecta"},{"id":590,"acronym":"RSPv6a","name":"Retrosplenial area, ventral part, layer 6a"},{"id":591,"acronym":"CLI","name":"Central linear nucleus raphe"},{"id":592,"acronym":"COApm1-2","name":"Cortical amygdalar area, posterior part, medial zone, layers 1-2"},{"id":593,"acronym":"VISp1","name":"Primary visual area, layer 1"},{"id":594,"acronym":"BSTtr","name":"Bed nuclei of the stria terminalis, posterior division, transverse nucleus"},{"id":595,"acronym":"fr","name":"fasciculus retroflexus"},{"id":596,"acronym":"NDB","name":"Diagonal band nucleus"},{"id":597,"acronym":"TTd","name":"Taenia tecta, dorsal part"},{"id":598,"acronym":"AUDv6b","name":"Ventral auditory area, layer 6b"},{"id":599,"acronym":"CM","name":"Central medial nucleus of the thalamus"},{"id":600,"acronym":"AUDd2/3","name":"Dorsal auditory area, layer 2/3"},{"id":601,"acronym":"VISal6a","name":"Anterolateral visual area, layer 6a"},{"id":602,"acronym":"BSTse","name":"Bed nuclei of the stria terminalis, posterior division, strial extension"},{"id":603,"acronym":"fi","name":"fimbria"},{"id":604,"acronym":"NI","name":"Nucleus incertus"},{"id":605,"acronym":"TTv","name":"Taenia tecta, ventral part"},{"id":606,"acronym":"RSPv2","name":"Retrosplenial area, ventral part, layer 2"},{"id":607,"acronym":"CN","name":"Cochlear nuclei"},{"id":608,"acronym":"ORBvl6a","name":"Orbital area, ventrolateral part, layer 6a"},{"id":609,"acronym":"SPA","name":"Subparafascicular area"},{"id":610,"acronym":"RSPd5","name":"Retrosplenial area, dorsal part, layer 5"},{"id":611,"acronym":"hbc","name":"habenular commissure"},{"id":612,"acronym":"NLL","name":"Nucleus of the lateral lemniscus"},{"id":613,"acronym":"VISl5","name":"Lateral visual area, layer 5"},{"id":614,"acronym":"TU","name":"Tuberal nucleus"},{"id":615,"acronym":"SNl","name":"Substantia nigra, lateral part"},{"id":616,"acronym":"CUN","name":"Cuneiform nucleus"},{"id":617,"acronym":"MDc","name":"Mediodorsal nucleus of the thalamus, central part"},{"id":618,"acronym":"hc","name":"hippocampal commissures"},{"id":619,"acronym":"NLOT","name":"Nucleus of the lateral olfactory tract"},{"id":620,"acronym":"ORBm5","name":"Orbital area, medial part, layer 5"},{"id":621,"acronym":"V","name":"Motor nucleus of trigeminal"},{"id":622,"acronym":"RSPv6b","name":"Retrosplenial area, ventral part, layer 6b"},{"id":623,"acronym":"CNU","name":"Cerebral nuclei"},{"id":624,"acronym":"IPF","name":"Interpeduncular fossa"},{"id":625,"acronym":"SSp-ul5","name":"Primary somatosensory area, upper limb, layer 5"},{"id":626,"acronym":"MDl","name":"Mediodorsal nucleus of the thalamus, lateral part"},{"id":627,"acronym":"hht","name":"hypothalamohypophysial tract"},{"id":628,"acronym":"NOT","name":"Nucleus of the optic tract"},{"id":629,"acronym":"VAL","name":"Ventral anterior-lateral complex of the thalamus"},{"id":630,"acronym":"ORBl5","name":"Orbital area, lateral part, layer 5"},{"id":631,"acronym":"COA","name":"Cortical amygdalar area"},{"id":632,"acronym":"DG-sg","name":"Dentate gyrus, granule cell layer"},{"id":633,"acronym":"cic","name":"inferior colliculus commissure"},{"id":634,"acronym":"NPC","name":"Nucleus of the posterior commissure"},{"id":635,"acronym":"PTLp4","name":"Posterior parietal association areas, layer 4"},{"id":636,"acronym":"MDm","name":"Mediodorsal nucleus of the thalamus, medial part"},{"id":637,"acronym":"VENT","name":"Ventral group of the dorsal thalamus"},{"id":638,"acronym":"GU6a","name":"Gustatory areas, layer 6a"},{"id":639,"acronym":"COAa","name":"Cortical amygdalar area, anterior part"},{"id":640,"acronym":"EV","name":"Efferent vestibular nucleus"},{"id":641,"acronym":"ias","name":"intermediate acoustic stria"},{"id":642,"acronym":"NTB","name":"Nucleus of the trapezoid body"},{"id":643,"acronym":"AUDpo2/3","name":"Posterior auditory area, layer 2/3"},{"id":644,"acronym":"MO6a","name":"Somatomotor areas, Layer 6a"},{"id":645,"acronym":"VERM","name":"Vermal regions"},{"id":646,"acronym":"DP5","name":"Dorsal peduncular area, layer 5"},{"id":647,"acronym":"COAp","name":"Cortical amygdalar area, posterior part"},{"id":648,"acronym":"MOp5","name":"Primary motor area, Layer 5"},{"id":649,"acronym":"VISal6b","name":"Anterolateral visual area, layer 6b"},{"id":650,"acronym":"jrb","name":"juxtarestiform body"},{"id":651,"acronym":"NTS","name":"Nucleus of the solitary tract"},{"id":652,"acronym":"PVHpml","name":"Paraventricular hypothalamic nucleus, magnocellular division, posterior magnocellular part, lateral zone"},{"id":653,"acronym":"VI","name":"Abducens nucleus"},{"id":654,"acronym":"SSp-n4","name":"Primary somatosensory area, nose, layer 4"},{"id":655,"acronym":"COApl","name":"Cortical amygdalar area, posterior part, lateral zone"},{"id":656,"acronym":"MOs1","name":"Secondary motor area, layer 1"},{"id":657,"acronym":"SSp-m2/3","name":"Primary somatosensory area, mouth, layer 2/3"},{"id":658,"acronym":"ll","name":"lateral lemniscus"},{"id":659,"acronym":"NTSce","name":"Nucleus of the solitary tract, central part"},{"id":660,"acronym":"PVHpmm","name":"Paraventricular hypothalamic nucleus, magnocellular division, posterior magnocellular part, medial zone"},{"id":661,"acronym":"VII","name":"Facial motor nucleus"},{"id":662,"acronym":"GU6b","name":"Gustatory areas, layer 6b"},{"id":663,"acronym":"COApm","name":"Cortical amygdalar area, posterior part, medial zone"},{"id":664,"acronym":"ENTm3","name":"Entorhinal area, medial part, dorsal zone, layer 3"},{"id":665,"acronym":"lot","name":"lateral olfactory tract, body"},{"id":666,"acronym":"NTSco","name":"Nucleus of the solitary tract, commissural part"},{"id":667,"acronym":"FRP2/3","name":"Frontal pole, layer 2/3"},{"id":668,"acronym":"DMHa","name":"Dorsomedial nucleus of the hypothalamus, anterior part"},{"id":669,"acronym":"VIS","name":"Visual areas"},{"id":670,"acronym":"SSp-tr2/3","name":"Primary somatosensory area, trunk, layer 2/3"},{"id":671,"acronym":"RSPagl1","name":"Retrosplenial area, lateral agranular part, layer 1"},{"id":672,"acronym":"CP","name":"Caudoputamen"},{"id":673,"acronym":"mp","name":"mammillary peduncle"},{"id":674,"acronym":"NTSge","name":"Nucleus of the solitary tract, gelatinous part"},{"id":675,"acronym":"AIv6a","name":"Agranular insular area, ventral part, layer 6a"},{"id":676,"acronym":"DMHp","name":"Dorsomedial nucleus of the hypothalamus, posterior part"},{"id":677,"acronym":"VISC","name":"Visceral area"},{"id":678,"acronym":"AUDd4","name":"Dorsal auditory area, layer 4"},{"id":679,"acronym":"CS","name":"Superior central nucleus raphe"},{"id":680,"acronym":"ORBvl6b","name":"Orbital area, ventrolateral part, layer 6b"},{"id":681,"acronym":"mtg","name":"mammillotegmental tract"},{"id":682,"acronym":"NTSl","name":"Nucleus of the solitary tract, lateral part"},{"id":683,"acronym":"PTLp5","name":"Posterior parietal association areas, layer 5"},{"id":684,"acronym":"DMHv","name":"Dorsomedial nucleus of the hypothalamus, ventral part"},{"id":685,"acronym":"VM","name":"Ventral medial nucleus of the thalamus"},{"id":686,"acronym":"SSp6a","name":"Primary somatosensory area, layer 6a"},{"id":687,"acronym":"RSPv5","name":"Retrosplenial area, ventral part, layer 5"},{"id":688,"acronym":"CTX","name":"Cerebral cortex"},{"id":689,"acronym":"VLPO","name":"Ventrolateral preoptic nucleus"},{"id":690,"acronym":"mtt","name":"mammillothalamic tract"},{"id":691,"acronym":"NTSm","name":"Nucleus of the solitary tract, medial part"},{"id":692,"acronym":"PERI5","name":"Perirhinal area, layer 5"},{"id":693,"acronym":"VMH","name":"Ventromedial hypothalamic nucleus"},{"id":694,"acronym":"AIv2/3","name":"Agranular insular area, ventral part, layer 2/3"},{"id":695,"acronym":"CTXpl","name":"Cortical plate"},{"id":696,"acronym":"AUDpo1","name":"Posterior auditory area, layer 1"},{"id":697,"acronym":"ml","name":"medial lemniscus"},{"id":698,"acronym":"OLF","name":"Olfactory areas"},{"id":699,"acronym":"AIv6b","name":"Agranular insular area, ventral part, layer 6b"},{"id":700,"acronym":"AHNa","name":"Anterior hypothalamic nucleus, anterior part"},{"id":701,"acronym":"VNC","name":"Vestibular nuclei"},{"id":702,"acronym":"SSp-n5","name":"Primary somatosensory area, nose, layer 5"},{"id":703,"acronym":"CTXsp","name":"Cortical subplate"},{"id":704,"acronym":"AIv1","name":"Agranular insular area, ventral part, layer 1"},{"id":705,"acronym":"mtV","name":"midbrain tract of the trigeminal nerve"},{"id":706,"acronym":"OP","name":"Olivary pretectal nucleus"},{"id":707,"acronym":"ILA1","name":"Infralimbic area, layer 1"},{"id":708,"acronym":"AHNc","name":"Anterior hypothalamic nucleus, central part"},{"id":709,"acronym":"VP","name":"Ventral posterior complex of the thalamus"},{"id":710,"acronym":"VIn","name":"abducens nerve"},{"id":711,"acronym":"CU","name":"Cuneate nucleus"},{"id":712,"acronym":"ENTm4","name":"Entorhinal area, medial part, dorsal zone, layer 4"},{"id":713,"acronym":"per","name":"perforant path"},{"id":714,"acronym":"ORB","name":"Orbital area"},{"id":715,"acronym":"ENTl2a","name":"Entorhinal area, lateral part, layer 2a"},{"id":716,"acronym":"AHNd","name":"Anterior hypothalamic nucleus, dorsal part"},{"id":717,"acronym":"XIn","name":"accessory spinal nerve"},{"id":718,"acronym":"VPL","name":"Ventral posterolateral nucleus of the thalamus"},{"id":719,"acronym":"SSp6b","name":"Primary somatosensory area, layer 6b"},{"id":720,"acronym":"DCN","name":"Dorsal column nuclei"},{"id":721,"acronym":"VISp4","name":"Primary visual area, layer 4"},{"id":722,"acronym":"pvbt","name":"periventricular bundle of the thalamus"},{"id":723,"acronym":"ORBl","name":"Orbital area, lateral part"},{"id":724,"acronym":"AHNp","name":"Anterior hypothalamic nucleus, posterior part"},{"id":725,"acronym":"VPLpc","name":"Ventral posterolateral nucleus of the thalamus, parvicellular part"},{"id":726,"acronym":"DG","name":"Dentate gyrus"},{"id":727,"acronym":"ENTm5","name":"Entorhinal area, medial part, dorsal zone, layer 5"},{"id":728,"acronym":"arb","name":"arbor vitae"},{"id":729,"acronym":"TEa6a","name":"Temporal association areas, layer 6a"},{"id":730,"acronym":"PIS","name":"pineal stalk"},{"id":731,"acronym":"ORBm","name":"Orbital area, medial part"},{"id":732,"acronym":"MMme","name":"Medial mammillary nucleus, median part"},{"id":733,"acronym":"VPM","name":"Ventral posteromedial nucleus of the thalamus"},{"id":734,"acronym":"DGcr","name":"Dentate gyrus crest"},{"id":735,"acronym":"AUDp1","name":"Primary auditory area, layer 1"},{"id":736,"acronym":"ctb","name":"central tegmental bundle"},{"id":737,"acronym":"fxpo","name":"postcommissural fornix"},{"id":738,"acronym":"ORBv","name":"Orbital area, ventral part"},{"id":739,"acronym":"ACA5","name":"Anterior cingulate area, layer 5"},{"id":740,"acronym":"MPNc","name":"Medial preoptic nucleus, central part"},{"id":741,"acronym":"VPMpc","name":"Ventral posteromedial nucleus of the thalamus, parvicellular part"},{"id":742,"acronym":"DGcr-mo","name":"Dentate gyrus crest, molecular layer"},{"id":743,"acronym":"ENTm6","name":"Entorhinal area, medial part, dorsal zone, layer 6"},{"id":744,"acronym":"cbc","name":"cerebellar commissure"},{"id":745,"acronym":"fxprg","name":"precommissural fornix, general"},{"id":746,"acronym":"ORBvl","name":"Orbital area, ventrolateral part"},{"id":747,"acronym":"ILA2","name":"Infralimbic area, layer 2"},{"id":748,"acronym":"MPNl","name":"Medial preoptic nucleus, lateral part"},{"id":749,"acronym":"VTA","name":"Ventral tegmental area"},{"id":750,"acronym":"VISpl1","name":"Posterolateral visual area, layer 1"},{"id":751,"acronym":"DGcr-po","name":"Dentate gyrus crest, polymorph layer"},{"id":752,"acronym":"cbp","name":"cerebellar peduncles"},{"id":753,"acronym":"pm","name":"principal mammillary tract"},{"id":754,"acronym":"OT","name":"Olfactory tubercle"},{"id":755,"acronym":"AUDv2/3","name":"Ventral auditory area, layer 2/3"},{"id":756,"acronym":"MPNm","name":"Medial preoptic nucleus, medial part"},{"id":757,"acronym":"VTN","name":"Ventral tegmental nucleus"},{"id":758,"acronym":"DGcr-sg","name":"Dentate gyrus crest, granule cell layer"},{"id":759,"acronym":"AUDpo4","name":"Posterior auditory area, layer 4"},{"id":760,"acronym":"epsc","name":"cerebral nuclei related"},{"id":761,"acronym":"VMHa","name":"Ventromedial hypothalamic nucleus, anterior part"},{"id":762,"acronym":"phpd","name":"propriohypothalamic pathways, dorsal"},{"id":763,"acronym":"OV","name":"Vascular organ of the lamina terminalis"},{"id":764,"acronym":"ENTl2b","name":"Entorhinal area, lateral part, layer 2b"},{"id":765,"acronym":"x","name":"Nucleus x"},{"id":766,"acronym":"DGlb","name":"Dentate gyrus lateral blade"},{"id":767,"acronym":"MOs5","name":"Secondary motor area, layer 5"},{"id":768,"acronym":"mfbc","name":"cerebrum related"},{"id":769,"acronym":"VMHc","name":"Ventromedial hypothalamic nucleus, central part"},{"id":770,"acronym":"phpl","name":"propriohypothalamic pathways, lateral"},{"id":771,"acronym":"P","name":"Pons"},{"id":772,"acronym":"ACAv5","name":"Anterior cingulate area, ventral part, layer 5"},{"id":773,"acronym":"XII","name":"Hypoglossal nucleus"},{"id":774,"acronym":"RSPagl5","name":"Retrosplenial area, lateral agranular part, layer 5"},{"id":775,"acronym":"DGlb-mo","name":"Dentate gyrus lateral blade, molecular layer"},{"id":776,"acronym":"cc","name":"corpus callosum"},{"id":777,"acronym":"VMHdm","name":"Ventromedial hypothalamic nucleus, dorsomedial part"},{"id":778,"acronym":"VISp5","name":"Primary visual area, layer 5"},{"id":779,"acronym":"phpm","name":"propriohypothalamic pathways, medial"},{"id":780,"acronym":"PA","name":"Posterior amygdalar nucleus"},{"id":781,"acronym":"y","name":"Nucleus y"},{"id":782,"acronym":"DGlb-po","name":"Dentate gyrus lateral blade, polymorph layer"},{"id":783,"acronym":"AId6a","name":"Agranular insular area, dorsal part, layer 6a"},{"id":784,"acronym":"cst","name":"corticospinal tract"},{"id":785,"acronym":"VMHvl","name":"Ventromedial hypothalamic nucleus, ventrolateral part"},{"id":786,"acronym":"TEa6b","name":"Temporal association areas, layer 6b"},{"id":787,"acronym":"phpv","name":"propriohypothalamic pathways, ventral"},{"id":788,"acronym":"PAA","name":"Piriform-amygdalar area"},{"id":789,"acronym":"z","name":"Nucleus z"},{"id":790,"acronym":"DGlb-sg","name":"Dentate gyrus lateral blade, granule cell layer"},{"id":791,"acronym":"AUDpo5","name":"Posterior auditory area, layer 5"},{"id":792,"acronym":"drt","name":"dorsal roots"},{"id":793,"acronym":"SSp1","name":"Primary somatosensory area, layer 1"},{"id":794,"acronym":"sptV","name":"spinal tract of the trigeminal nerve"},{"id":795,"acronym":"PAG","name":"Periaqueductal gray"},{"id":796,"acronym":"A13","name":"Dopaminergic A13 group"},{"id":797,"acronym":"ZI","name":"Zona incerta"},{"id":798,"acronym":"VIIn","name":"facial nerve"},{"id":799,"acronym":"DGmb","name":"Dentate gyrus medial blade"},{"id":800,"acronym":"AIv5","name":"Agranular insular area, ventral part, layer 5"},{"id":801,"acronym":"VIS1","name":"Visual areas, layer 1"},{"id":802,"acronym":"sm","name":"stria medullaris"},{"id":803,"acronym":"PAL","name":"Pallidum"},{"id":804,"acronym":"FF","name":"Fields of Forel"},{"id":805,"acronym":"VISpm1","name":"posteromedial visual area, layer 1"},{"id":806,"acronym":"SSs2/3","name":"Supplemental somatosensory area, layer 2/3"},{"id":807,"acronym":"DGmb-mo","name":"Dentate gyrus medial blade, molecular layer"},{"id":808,"acronym":"IXn","name":"glossopharyngeal nerve"},{"id":809,"acronym":"PALc","name":"Pallidum, caudal region"},{"id":810,"acronym":"ACAv6a","name":"Anterior cingulate area, ventral part, 6a"},{"id":811,"acronym":"ICc","name":"Inferior colliculus, central nucleus"},{"id":812,"acronym":"dscp","name":"superior cerebellar peduncle decussation"},{"id":813,"acronym":"XIIn","name":"hypoglossal nerve"},{"id":814,"acronym":"DP","name":"Dorsal peduncular area"},{"id":815,"acronym":"DGmb-po","name":"Dentate gyrus medial blade, polymorph layer"},{"id":816,"acronym":"AUDp4","name":"Primary auditory area, layer 4"},{"id":817,"acronym":"supa","name":"supraoptic commissures, anterior"},{"id":818,"acronym":"PALd","name":"Pallidum, dorsal region"},{"id":819,"acronym":"ACAv6b","name":"Anterior cingulate area, ventral part, 6b"},{"id":820,"acronym":"ICd","name":"Inferior colliculus, dorsal nucleus"},{"id":821,"acronym":"VISp2/3","name":"Primary visual area, layer 2/3"},{"id":822,"acronym":"RHP","name":"Retrohippocampal region"},{"id":823,"acronym":"DGmb-sg","name":"Dentate gyrus medial blade, granule cell layer"},{"id":824,"acronym":"mfsbshy","name":"hypothalamus related"},{"id":825,"acronym":"supd","name":"supraoptic commissures, dorsal"},{"id":826,"acronym":"PALm","name":"Pallidum, medial region"},{"id":827,"acronym":"ILA5","name":"Infralimbic area, layer 5"},{"id":828,"acronym":"ICe","name":"Inferior colliculus, external nucleus"},{"id":829,"acronym":"SUBd-m","name":"Subiculum, dorsal part, molecular layer"},{"id":830,"acronym":"DMH","name":"Dorsomedial nucleus of the hypothalamus"},{"id":831,"acronym":"AId6b","name":"Agranular insular area, dorsal part, layer 6b"},{"id":832,"acronym":"IIIn","name":"oculomotor nerve"},{"id":833,"acronym":"supv","name":"supraoptic commissures, ventral"},{"id":834,"acronym":"SCzo","name":"Superior colliculus, zonal layer"},{"id":835,"acronym":"PALv","name":"Pallidum, ventral region"},{"id":836,"acronym":"ECT1","name":"Ectorhinal area/Layer 1"},{"id":837,"acronym":"SUBd-sr","name":"Subiculum, dorsal part, stratum radiatum"},{"id":838,"acronym":"SSp-n2/3","name":"Primary somatosensory area, nose, layer 2/3"},{"id":839,"acronym":"DMX","name":"Dorsal motor nucleus of the vagus nerve"},{"id":840,"acronym":"In","name":"olfactory nerve"},{"id":841,"acronym":"tb","name":"trapezoid body"},{"id":842,"acronym":"SCsg","name":"Superior colliculus, superficial gray layer"},{"id":843,"acronym":"PAR","name":"Parasubiculum"},{"id":844,"acronym":"MOp6a","name":"Primary motor area, Layer 6a"},{"id":845,"acronym":"SUBd-sp","name":"Subiculum, dorsal part, pyramidal layer"},{"id":846,"acronym":"DN","name":"Dentate nucleus"},{"id":847,"acronym":"AUDp5","name":"Primary auditory area, layer 5"},{"id":848,"acronym":"IIn","name":"optic nerve"},{"id":849,"acronym":"VISC6b","name":"Visceral area, layer 6b"},{"id":850,"acronym":"uf","name":"uncinate fascicle"},{"id":851,"acronym":"SCop","name":"Superior colliculus, optic layer"},{"id":852,"acronym":"PARN","name":"Parvicellular reticular nucleus"},{"id":853,"acronym":"SUBv-m","name":"Subiculum, ventral part, molecular layer"},{"id":854,"acronym":"SSp-ul2/3","name":"Primary somatosensory area, upper limb, layer 2/3"},{"id":855,"acronym":"rst","name":"retriculospinal tract"},{"id":856,"acronym":"DORpm","name":"Thalamus, polymodal 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4"},{"id":870,"acronym":"SUBv-sp","name":"Subiculum, ventral part, pyramidal layer"},{"id":871,"acronym":"sst","name":"spinothalamic tract"},{"id":872,"acronym":"DR","name":"Dorsal nucleus raphe"},{"id":873,"acronym":"SSs1","name":"Supplemental somatosensory area, layer 1"},{"id":874,"acronym":"PBG","name":"Parabigeminal nucleus"},{"id":875,"acronym":"PBle","name":"Parabrachial nucleus, lateral division, external lateral part"},{"id":876,"acronym":"aot","name":"accessory optic tract"},{"id":877,"acronym":"tsp","name":"tectospinal pathway"},{"id":878,"acronym":"SSp-m1","name":"Primary somatosensory area, mouth, layer 1"},{"id":879,"acronym":"RSPd","name":"Retrosplenial area, dorsal part"},{"id":880,"acronym":"DTN","name":"Dorsal tegmental nucleus"},{"id":881,"acronym":"PBl","name":"Parabrachial nucleus, lateral division"},{"id":882,"acronym":"MOp6b","name":"Primary motor area, Layer 6b"},{"id":883,"acronym":"PBls","name":"Parabrachial nucleus, lateral division, superior lateral part"},{"id":884,"acronym":"amc","name":"amygdalar capsule"},{"id":885,"acronym":"tn","name":"terminal nerve"},{"id":886,"acronym":"RSPv","name":"Retrosplenial area, ventral part"},{"id":887,"acronym":"ECO","name":"Efferent cochlear group"},{"id":888,"acronym":"PERI2/3","name":"Perirhinal area, layer 2/3"},{"id":889,"acronym":"SSp-n6a","name":"Primary somatosensory area, nose, layer 6a"},{"id":890,"acronym":"PBm","name":"Parabrachial nucleus, medial division"},{"id":891,"acronym":"PBlv","name":"Parabrachial nucleus, lateral division, ventral lateral part"},{"id":892,"acronym":"apd","name":"ansa peduncularis"},{"id":893,"acronym":"SSs6b","name":"Supplemental somatosensory area, layer 6b"},{"id":894,"acronym":"RSPagl","name":"Retrosplenial area, lateral agranular part"},{"id":895,"acronym":"ECT","name":"Ectorhinal area"},{"id":896,"acronym":"lfbst","name":"thalamus related"},{"id":897,"acronym":"VISC1","name":"Visceral area, layer 1"},{"id":898,"acronym":"PCG","name":"Pontine central gray"},{"id":899,"acronym":"PBme","name":"Parabrachial nucleus, medial division, external medial part"},{"id":900,"acronym":"aco","name":"anterior commissure, olfactory limb"},{"id":901,"acronym":"Vn","name":"trigeminal nerve"},{"id":902,"acronym":"VISpl5","name":"Posterolateral visual area, layer 5"},{"id":903,"acronym":"ECU","name":"External cuneate nucleus"},{"id":904,"acronym":"MSC","name":"Medial septal complex"},{"id":905,"acronym":"VISal2/3","name":"Anterolateral visual area, layer 2/3"},{"id":906,"acronym":"RSPagl6a","name":"Retrosplenial area, lateral agranular part, layer 6a"},{"id":907,"acronym":"PCN","name":"Paracentral nucleus"},{"id":908,"acronym":"act","name":"anterior commissure, temporal limb"},{"id":909,"acronym":"ENT","name":"Entorhinal area"},{"id":910,"acronym":"ORBm6a","name":"Orbital area, medial part, layer 6a"},{"id":911,"acronym":"IVn","name":"trochlear nerve"},{"id":912,"acronym":"LING","name":"Lingula (I)"},{"id":913,"acronym":"VIS4","name":"Visual areas, layer 4"},{"id":914,"acronym":"PD","name":"Posterodorsal preoptic nucleus"},{"id":915,"acronym":"PBmm","name":"Parabrachial nucleus, medial division, medial medial part"},{"id":916,"acronym":"bsc","name":"brachium of the superior colliculus"},{"id":917,"acronym":"Xn","name":"vagus nerve"},{"id":918,"acronym":"ENTl","name":"Entorhinal area, lateral part"},{"id":919,"acronym":"ACAd6a","name":"Anterior cingulate area, dorsal part, layer 6a"},{"id":920,"acronym":"CENT","name":"Central lobule"},{"id":921,"acronym":"SSp5","name":"Primary somatosensory area, layer 5"},{"id":922,"acronym":"PERI","name":"Perirhinal area"},{"id":923,"acronym":"PBmv","name":"Parabrachial nucleus, medial division, ventral medial part"},{"id":924,"acronym":"cpd","name":"cerebal peduncle"},{"id":925,"acronym":"vrt","name":"ventral roots"},{"id":926,"acronym":"ENTm","name":"Entorhinal area, medial part, dorsal zone"},{"id":927,"acronym":"ACAd6b","name":"Anterior cingulate area, dorsal part, layer 6b"},{"id":928,"acronym":"CUL","name":"Culmen"},{"id":929,"acronym":"SSp-n6b","name":"Primary somatosensory area, nose, layer 6b"},{"id":930,"acronym":"PF","name":"Parafascicular nucleus"},{"id":931,"acronym":"PG","name":"Pontine gray"},{"id":932,"acronym":"cett","name":"cervicothalamic tract"},{"id":933,"acronym":"VIIIn","name":"vestibulocochlear nerve"},{"id":934,"acronym":"ENTmv","name":"Entorhinal area, medial part, ventral zone"},{"id":935,"acronym":"ACAd1","name":"Anterior cingulate area, dorsal part, layer 1"},{"id":936,"acronym":"DEC","name":"Declive (VI)"},{"id":937,"acronym":"VIS5","name":"Visual areas, layer 5"},{"id":938,"acronym":"PGRN","name":"Paragigantocellular reticular nucleus"},{"id":939,"acronym":"AMBd","name":"Nucleus ambiguus, dorsal division"},{"id":940,"acronym":"cing","name":"cingulum bundle"},{"id":941,"acronym":"vsp","name":"vestibulospinal pathway"},{"id":942,"acronym":"EP","name":"Endopiriform nucleus"},{"id":943,"acronym":"MOp2/3","name":"Primary motor 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(IX)"},{"id":958,"acronym":"EPI","name":"Epithalamus"},{"id":959,"acronym":"AUDv1","name":"Ventral auditory area, layer 1"},{"id":960,"acronym":"cbf","name":"cerebellum related fiber tracts"},{"id":961,"acronym":"PIR","name":"Piriform area"},{"id":962,"acronym":"MOs2/3","name":"Secondary motor area, layer 2/3"},{"id":963,"acronym":"LRNp","name":"Lateral reticular nucleus, parvicellular part"},{"id":964,"acronym":"ee","name":"corpus callosum, extreme capsule"},{"id":965,"acronym":"RSPagl2/3","name":"Retrosplenial area, lateral agranular part, layer 2/3"},{"id":966,"acronym":"EPv","name":"Endopiriform nucleus, ventral part"},{"id":967,"acronym":"cm","name":"cranial nerves"},{"id":968,"acronym":"NOD","name":"Nodulus (X)"},{"id":969,"acronym":"ORBvl1","name":"Orbital area, ventrolateral part, layer 1"},{"id":970,"acronym":"PGRNd","name":"Paragigantocellular reticular nucleus, dorsal part"},{"id":971,"acronym":"fp","name":"corpus callosum, posterior forceps"},{"id":972,"acronym":"PL","name":"Prelimbic area"},{"id":973,"acronym":"VISl2/3","name":"Lateral visual area, layer 2/3"},{"id":974,"acronym":"SSp-m5","name":"Primary somatosensory area, mouth, layer 5"},{"id":975,"acronym":"EW","name":"Edinger-Westphal nucleus"},{"id":976,"acronym":"CENT2","name":"Lobule II"},{"id":977,"acronym":"ECT6a","name":"Ectorhinal area/Layer 6a"},{"id":978,"acronym":"PGRNl","name":"Paragigantocellular reticular nucleus, lateral part"},{"id":979,"acronym":"ccr","name":"corpus callosum, rostrum"},{"id":980,"acronym":"PMd","name":"Dorsal premammillary nucleus"},{"id":981,"acronym":"SSp-bfd1","name":"Primary somatosensory area, barrel field, layer 1"},{"id":982,"acronym":"FC","name":"Fasciola cinerea"},{"id":983,"acronym":"lfbs","name":"lateral forebrain bundle system"},{"id":984,"acronym":"CENT3","name":"Lobule III"},{"id":985,"acronym":"MOp","name":"Primary motor area"},{"id":986,"acronym":"ccs","name":"corpus callosum, splenium"},{"id":987,"acronym":"P-mot","name":"Pons, motor related"},{"id":988,"acronym":"ECT5","name":"Ectorhinal area/Layer 5"},{"id":989,"acronym":"FN","name":"Fastigial nucleus"},{"id":990,"acronym":"AUDv4","name":"Ventral auditory area, layer 4"},{"id":991,"acronym":"mfbs","name":"medial forebrain bundle system"},{"id":992,"acronym":"CUL4","name":"Lobule IV"},{"id":993,"acronym":"MOs","name":"Secondary motor area"},{"id":994,"acronym":"cbt","name":"corticobulbar tract"},{"id":995,"acronym":"PMR","name":"Paramedian reticular nucleus"},{"id":996,"acronym":"AId1","name":"Agranular insular area, dorsal part, layer 1"},{"id":997,"acronym":"root","name":"root"},{"id":998,"acronym":"FS","name":"Fundus of striatum"},{"id":999,"acronym":"ENTl2/3","name":"Entorhinal area, lateral part, layer 2/3"},{"id":1000,"acronym":"eps","name":"extrapyramidal fiber systems"},{"id":1001,"acronym":"CUL5","name":"Lobule V"},{"id":1002,"acronym":"AUDp","name":"Primary auditory area"},{"id":1003,"acronym":"cpt","name":"corticopontine tract"},{"id":1004,"acronym":"PMv","name":"Ventral premammillary nucleus"},{"id":1005,"acronym":"AUDp6b","name":"Primary auditory area, layer 6b"},{"id":1006,"acronym":"SSp-tr1","name":"Primary somatosensory area, trunk, layer 1"},{"id":1007,"acronym":"SIM","name":"Simple lobule"},{"id":1008,"acronym":"GENd","name":"Geniculate group, dorsal thalamus"},{"id":1009,"acronym":"fiber tracts","name":"fiber tracts"},{"id":1010,"acronym":"VISC4","name":"Visceral area, layer 4"},{"id":1011,"acronym":"AUDd","name":"Dorsal auditory area"},{"id":1012,"acronym":"crt","name":"corticorubral tract"},{"id":1014,"acronym":"GENv","name":"Geniculate group, ventral thalamus"},{"id":1015,"acronym":"ACAd5","name":"Anterior cingulate area, dorsal part, layer 5"},{"id":1016,"acronym":"onl","name":"olfactory nerve layer of main olfactory bulb"},{"id":1017,"acronym":"AN","name":"Ansiform lobule"},{"id":1018,"acronym":"AUDv","name":"Ventral auditory area"},{"id":1019,"acronym":"cstc","name":"corticospinal tract, crossed"},{"id":1020,"acronym":"PO","name":"Posterior complex of the thalamus"},{"id":1021,"acronym":"MOs6a","name":"Secondary motor area, layer 6a"},{"id":1022,"acronym":"GPe","name":"Globus pallidus, external segment"},{"id":1023,"acronym":"AUDv5","name":"Ventral auditory area, layer 5"},{"id":1024,"acronym":"grv","name":"grooves"},{"id":1025,"acronym":"PRM","name":"Paramedian lobule"},{"id":1026,"acronym":"SSp-ul6b","name":"Primary somatosensory area, upper limb, layer 6b"},{"id":1027,"acronym":"AUDpo","name":"Posterior auditory area"},{"id":1028,"acronym":"cstu","name":"corticospinal tract, uncrossed"},{"id":1029,"acronym":"POL","name":"Posterior limiting nucleus of the thalamus"},{"id":1030,"acronym":"SSp-ll1","name":"Primary somatosensory area, lower limb, layer 1"},{"id":1031,"acronym":"GPi","name":"Globus pallidus, internal segment"},{"id":1032,"acronym":"grv of CTX","name":"grooves of the cerebral 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6a"},{"id":182305713,"acronym":"SSp-un6b","name":"Primary somatosensory area, unassigned, layer 6b"},{"id":304325711,"acronym":"retina","name":"retina"},{"id":312782546,"acronym":"VISa","name":"Anterior area"},{"id":312782550,"acronym":"VISa1","name":"Anterior area, layer 1"},{"id":312782554,"acronym":"VISa2/3","name":"Anterior area, layer 2/3"},{"id":312782558,"acronym":"VISa4","name":"Anterior area, layer 4"},{"id":312782562,"acronym":"VISa5","name":"Anterior area, layer 5"},{"id":312782566,"acronym":"VISa6a","name":"Anterior area, layer 6a"},{"id":312782570,"acronym":"VISa6b","name":"Anterior area, layer 6b"},{"id":312782574,"acronym":"VISli","name":"Laterointermediate area"},{"id":312782578,"acronym":"VISli1","name":"Laterointermediate area, layer 1"},{"id":312782582,"acronym":"VISli2/3","name":"Laterointermediate area, layer 2/3"},{"id":312782586,"acronym":"VISli4","name":"Laterointermediate area, layer 4"},{"id":312782590,"acronym":"VISli5","name":"Laterointermediate area, layer 5"},{"id":312782594,"acronym":"VISli6a","name":"Laterointermediate area, layer 6a"},{"id":312782598,"acronym":"VISli6b","name":"Laterointermediate area, layer 6b"},{"id":312782604,"acronym":"VISrl1","name":"Rostrolateral area, layer 1"},{"id":312782608,"acronym":"VISrl2/3","name":"Rostrolateral area, layer 2/3"},{"id":312782612,"acronym":"VISrl4","name":"Rostrolateral area, layer 4"},{"id":312782616,"acronym":"VISrl5","name":"Rostrolateral area, layer 5"},{"id":312782620,"acronym":"VISrl6a","name":"Rostrolateral area, layer 6a"},{"id":312782624,"acronym":"VISrl6b","name":"Rostrolateral area, layer 6b"},{"id":312782628,"acronym":"VISpor","name":"Postrhinal area"},{"id":312782632,"acronym":"VISpor1","name":"Postrhinal area, layer 1"},{"id":312782636,"acronym":"VISpor2/3","name":"Postrhinal area, layer 2/3"},{"id":312782640,"acronym":"VISpor4","name":"Postrhinal area, layer 4"},{"id":312782644,"acronym":"VISpor5","name":"Postrhinal area, layer 5"},{"id":312782648,"acronym":"VISpor6a","name":"Postrhinal area, layer 6a"},{"id":312782652,"acronym":"VISpor6b","name":"Postrhinal area, layer 6b"},{"id":480149202,"acronym":"VISrll","name":"Rostrolateral lateral visual area"},{"id":480149206,"acronym":"VISrll1","name":"Rostrolateral lateral visual area, layer 1"},{"id":480149210,"acronym":"VISrll2/3","name":"Rostrolateral lateral visual area, layer 2/3"},{"id":480149214,"acronym":"VISrll4","name":"Rostrolateral lateral visual area, layer 4"},{"id":480149218,"acronym":"VISrll5","name":"Rostrolateral lateral visual area,layer 5"},{"id":480149222,"acronym":"VISrll6a","name":"Rostrolateral lateral visual area, layer 6a"},{"id":480149226,"acronym":"VISrll6b","name":"Rostrolateral lateral visual area, layer 6b"},{"id":480149230,"acronym":"VISlla","name":"Laterolateral anterior visual area"},{"id":480149234,"acronym":"VISlla1","name":"Laterolateral anterior visual area, layer 1"},{"id":480149238,"acronym":"VISlla2/3","name":"Laterolateral anterior visual area, layer 2/3"},{"id":480149242,"acronym":"VISlla4","name":"Laterolateral anterior visual area, layer 4"},{"id":480149246,"acronym":"VISlla5","name":"Laterolateral anterior visual area,layer 5"},{"id":480149250,"acronym":"VISlla6a","name":"Laterolateral anterior visual area, layer 6a"},{"id":480149254,"acronym":"VISlla6b","name":"Laterolateral anterior visual area, layer 6b"},{"id":480149258,"acronym":"VISmma","name":"Mediomedial anterior visual area"},{"id":480149262,"acronym":"VISmma1","name":"Mediomedial anterior visual area, layer 1"},{"id":480149266,"acronym":"VISmma2/3","name":"Mediomedial anterior visual area, layer 2/3"},{"id":480149270,"acronym":"VISmma4","name":"Mediomedial anterior visual area, layer 4"},{"id":480149274,"acronym":"VISmma5","name":"Mediomedial anterior visual area,layer 5"},{"id":480149278,"acronym":"VISmma6a","name":"Mediomedial anterior visual area, layer 6a"},{"id":480149282,"acronym":"VISmma6b","name":"Mediomedial anterior visual area, layer 6b"},{"id":480149286,"acronym":"VISmmp","name":"Mediomedial posterior visual area"},{"id":480149290,"acronym":"VISmmp1","name":"Mediomedial posterior visual area, layer 1"},{"id":480149294,"acronym":"VISmmp2/3","name":"Mediomedial posterior visual area, layer 2/3"},{"id":480149298,"acronym":"VISmmp4","name":"Mediomedial posterior visual area, layer 4"},{"id":480149302,"acronym":"VISmmp5","name":"Mediomedial posterior visual area,layer 5"},{"id":480149306,"acronym":"VISmmp6a","name":"Mediomedial posterior visual area, layer 6a"},{"id":480149310,"acronym":"VISmmp6b","name":"Mediomedial posterior visual area, layer 6b"},{"id":480149314,"acronym":"VISm","name":"Medial visual area"},{"id":480149318,"acronym":"VISm1","name":"Medial visual area, layer 1"},{"id":480149322,"acronym":"VISm2/3","name":"Medial visual area, layer 2/3"},{"id":480149326,"acronym":"VISm4","name":"Medial visual area, layer 4"},{"id":480149330,"acronym":"VISm5","name":"Medial visual area,layer 5"},{"id":480149334,"acronym":"VISm6a","name":"Medial visual area, layer 6a"},{"id":480149338,"acronym":"VISm6b","name":"Medial visual area, layer 6b"},{"id":484682470,"acronym":"ProS","name":"Prosubiculum"},{"id":484682475,"acronym":"ProSd","name":"Prosubiculum, dorsal part"},{"id":484682479,"acronym":"ProSd-m","name":"Prosubiculum, dorsal part, molecular layer"},{"id":484682483,"acronym":"ProSd-sp","name":"Prosubiculum, dorsal part, pyramidal layer"},{"id":484682487,"acronym":"ProSd-sr","name":"Prosubiculum, dorsal part, stratum radiatum"},{"id":484682492,"acronym":"ProSv","name":"Prosubiculum, ventral part"},{"id":484682496,"acronym":"ProSv-m","name":"Prosubiculum, ventral part, molecular layer"},{"id":484682500,"acronym":"ProSv-sp","name":"Prosubiculum, ventral part, pyramidal layer"},{"id":484682504,"acronym":"Prosv-sr","name":"Prosubiculum, ventral part, stratum radiatum"},{"id":484682508,"acronym":"APr","name":"Area prostriata"},{"id":484682512,"acronym":"scwm","name":"supra-callosal cerebral white matter"},{"id":484682516,"acronym":"ccb","name":"corpus callosum, body"},{"id":484682520,"acronym":"or","name":"optic radiation"},{"id":484682524,"acronym":"ar","name":"auditory radiation"},{"id":484682528,"acronym":"stc","name":"commissural branch of stria terminalis"},{"id":496345664,"acronym":"LGd-sh","name":"Dorsal part of the lateral geniculate complex, shell"},{"id":496345668,"acronym":"LGd-co","name":"Dorsal part of the lateral geniculate complex, core"},{"id":496345672,"acronym":"LGd-ip","name":"Dorsal part of the lateral geniculate complex, ipsilateral zone"},{"id":526157192,"acronym":"FRP5","name":"Frontal pole, layer 5"},{"id":526157196,"acronym":"FRP6a","name":"Frontal pole, layer 6a"},{"id":526322264,"acronym":"FRP6b","name":"Frontal pole, layer 6b"},{"id":527696977,"acronym":"ORBm6b","name":"Orbital area, medial part, layer 6b"},{"id":549009199,"acronym":"LSS","name":"Lateral strip of striatum"},{"id":549009203,"acronym":"RPF","name":"Retroparafascicular nucleus"},{"id":549009207,"acronym":"InCo","name":"Intercollicular nucleus"},{"id":549009211,"acronym":"MA3","name":"Medial accesory oculomotor nucleus"},{"id":549009215,"acronym":"P5","name":"Peritrigeminal zone"},{"id":549009219,"acronym":"Acs5","name":"Accessory trigeminal nucleus"},{"id":549009223,"acronym":"PC5","name":"Parvicellular motor 5 nucleus"},{"id":549009227,"acronym":"I5","name":"Intertrigeminal nucleus"},{"id":560581551,"acronym":"Eth","name":"Ethmoid nucleus of the thalamus"},{"id":560581555,"acronym":"REth","name":"Retroethmoid nucleus"},{"id":560581559,"acronym":"Xi","name":"Xiphoid thalamic nucleus"},{"id":560581563,"acronym":"PIL","name":"Posterior intralaminar thalamic nucleus"},{"id":563807435,"acronym":"PoT","name":"Posterior triangular thalamic nucleus"},{"id":563807439,"acronym":"IntG","name":"Intermediate geniculate nucleus"},{"id":576073699,"acronym":"VMPO","name":"Ventromedial preoptic nucleus"},{"id":576073704,"acronym":"PeF","name":"Perifornical nucleus"},{"id":589508447,"acronym":"HATA","name":"Hippocampo-amygdalar transition area"},{"id":589508451,"acronym":"Pa5","name":"Paratrigeminal nucleus"},{"id":589508455,"acronym":"VeCB","name":"Vestibulocerebellar nucleus"},{"id":599626923,"acronym":"SCO","name":"Subcommissural organ"},{"id":599626927,"acronym":"PDTg","name":"Posterodorsal tegmental nucleus"},{"id":606826647,"acronym":"MMl","name":"Medial mammillary nucleus, lateral part"},{"id":606826651,"acronym":"MMm","name":"Medial mammillary nucleus, medial part"},{"id":606826655,"acronym":"MMp","name":"Medial mammillary nucleus, posterior part"},{"id":606826659,"acronym":"MMd","name":"Medial mammillary nucleus, dorsal part"},{"id":606826663,"acronym":"Pa4","name":"Paratrochlear nucleus"},{"id":607344830,"acronym":"PN","name":"Paranigral nucleus"},{"id":607344834,"acronym":"IPR","name":"Interpeduncular nucleus, rostral"},{"id":607344838,"acronym":"IPC","name":"Interpeduncular nucleus, caudal"},{"id":607344842,"acronym":"IPA","name":"Interpeduncular nucleus, apical"},{"id":607344846,"acronym":"IPL","name":"Interpeduncular nucleus, lateral"},{"id":607344850,"acronym":"IPI","name":"Interpeduncular nucleus, intermediate"},{"id":607344854,"acronym":"IPDM","name":"Interpeduncular nucleus, dorsomedial"},{"id":607344858,"acronym":"IPDL","name":"Interpeduncular nucleus, dorsolateral"},{"id":607344862,"acronym":"IPRL","name":"Interpeduncular nucleus, rostrolateral"},{"id":614454277,"acronym":"Su3","name":"Supraoculomotor periaqueductal gray"}] diff --git a/dandi/data/generate_allen_structures.py b/dandi/data/generate_allen_structures.py new file mode 100644 index 000000000..382bf80a0 --- /dev/null +++ b/dandi/data/generate_allen_structures.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 +"""Regenerate allen_ccf_structures.json from Allen Brain Map API. + +Run: python -m dandi.data.generate_allen_structures +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import requests + + +def _flatten(node: dict, out: list[dict]) -> None: + out.append({"id": node["id"], "acronym": node["acronym"], "name": node["name"]}) + for child in node.get("children", []): + _flatten(child, out) + + +def main() -> None: + url = "http://api.brain-map.org/api/v2/structure_graph_download/1.json" + resp = requests.get(url, timeout=30) + resp.raise_for_status() + data = resp.json() + structures: list[dict] = [] + root = data["msg"][0] + _flatten(root, structures) + structures.sort(key=lambda s: s["id"]) + out_path = Path(__file__).with_name("allen_ccf_structures.json") + with open(out_path, "w") as f: + json.dump(structures, f, separators=(",", ":")) + print(f"Wrote {len(structures)} structures to {out_path}") + + +if __name__ == "__main__": + main() diff --git a/dandi/metadata/brain_areas.py b/dandi/metadata/brain_areas.py new file mode 100644 index 000000000..11de60ed7 --- /dev/null +++ b/dandi/metadata/brain_areas.py @@ -0,0 +1,221 @@ +from __future__ import annotations + +import ast +from functools import lru_cache +import json +from pathlib import Path +import re +from typing import Any + +from dandischema import models + +from .. import get_logger + +lgr = get_logger() + +MBAO_URI_TEMPLATE = "http://purl.obolibrary.org/obo/MBA_{}" + +# Values that should be treated as missing / uninformative +_TRIVIAL_VALUES = frozenset( + { + "", + "unknown", + "none", + "n/a", + "na", + "null", + "unspecified", + "not available", + "not applicable", + "brain", + } +) + + +@lru_cache(maxsize=1) +def _load_allen_structures() -> list[dict[str, Any]]: + """Load the bundled Allen CCF structures JSON.""" + data_path = ( + Path(__file__).resolve().parent.parent / "data" / "allen_ccf_structures.json" + ) + with open(data_path) as f: + structures: list[dict[str, Any]] = json.load(f) + return structures + + +@lru_cache(maxsize=1) +def _build_lookup_dicts() -> ( + tuple[dict[str, dict], dict[str, dict], dict[str, dict], dict[str, dict]] +): + """Build lookup dictionaries for Allen CCF structures. + + Returns + ------- + tuple of 4 dicts + (acronym_exact, acronym_lower, name_exact, name_lower) + """ + structures = _load_allen_structures() + acronym_exact: dict[str, dict] = {} + acronym_lower: dict[str, dict] = {} + name_exact: dict[str, dict] = {} + name_lower: dict[str, dict] = {} + for s in structures: + acr = s["acronym"] + name = s["name"] + # First match wins (structures are sorted by id) + if acr not in acronym_exact: + acronym_exact[acr] = s + acr_low = acr.lower() + if acr_low not in acronym_lower: + acronym_lower[acr_low] = s + if name not in name_exact: + name_exact[name] = s + name_low = name.lower() + if name_low not in name_lower: + name_lower[name_low] = s + return acronym_exact, acronym_lower, name_exact, name_lower + + +def _parse_location_string(location: str) -> list[str]: + """Parse a raw NWB location string into area tokens. + + Handles: + - Simple strings: ``"VISp"`` + - Dict literals: ``"{'area': 'VISp', 'depth': '20'}"`` + - Key-value pairs: ``"area: VISp, depth: 175"`` + - Comma-separated lists: ``"VISp,VISrl,VISlm"`` + """ + location = location.strip() + if not location or location.lower() in _TRIVIAL_VALUES: + return [] + + # Try dict literal (e.g. "{'area': 'VISp', 'depth': 20}") + if location.startswith("{"): + try: + d = ast.literal_eval(location) + if isinstance(d, dict): + # Look for known area keys + for key in ("area", "location", "region", "brain_area", "brain_region"): + val = d.get(key) + if val is not None: + val = str(val).strip() + if val and val.lower() not in _TRIVIAL_VALUES: + return [val] + # If no known key, return all string values that are non-trivial + tokens = [] + for val in d.values(): + val = str(val).strip() + if val and val.lower() not in _TRIVIAL_VALUES: + # Skip purely numeric values (e.g. depth) + try: + float(val) + except ValueError: + tokens.append(val) + return tokens + except (ValueError, SyntaxError): + pass # Not a valid dict literal; fall through to other parsers + + # Try key-value format (e.g. "area: VISp, depth: 175") + if re.search(r"\w+\s*:", location) and "://" not in location: + pairs = re.split(r",\s*", location) + kv: dict[str, str] = {} + for pair in pairs: + m = re.match(r"(\w+)\s*:\s*(.+)", pair.strip()) + if m: + kv[m.group(1).lower()] = m.group(2).strip() + if kv: + for key in ("area", "location", "region", "brain_area", "brain_region"): + val = kv.get(key) + if val is not None and val.lower() not in _TRIVIAL_VALUES: + return [val] + # Fall through — return non-trivial, non-numeric values + tokens = [] + for val in kv.values(): + if val.lower() not in _TRIVIAL_VALUES: + try: + float(val) + except ValueError: + tokens.append(val) + if tokens: + return tokens + + # Comma-separated list + if "," in location: + tokens = [t.strip() for t in location.split(",")] + return [t for t in tokens if t and t.lower() not in _TRIVIAL_VALUES] + + # Simple string + return [location] + + +def match_location_to_allen(token: str) -> models.Anatomy | None: + """Match a single location token against Allen CCF structures. + + Tries exact acronym, case-insensitive acronym, exact name, + case-insensitive name in that order. + + Returns + ------- + models.Anatomy or None + """ + acronym_exact, acronym_lower, name_exact, name_lower = _build_lookup_dicts() + token_stripped = token.strip() + if not token_stripped: + return None + + # 1. Exact acronym match + s = acronym_exact.get(token_stripped) + if s is not None: + return _structure_to_anatomy(s) + + # 2. Case-insensitive acronym match + s = acronym_lower.get(token_stripped.lower()) + if s is not None: + return _structure_to_anatomy(s) + + # 3. Exact name match + s = name_exact.get(token_stripped) + if s is not None: + return _structure_to_anatomy(s) + + # 4. Case-insensitive name match + s = name_lower.get(token_stripped.lower()) + if s is not None: + return _structure_to_anatomy(s) + + lgr.debug("Could not match brain location %r to Allen CCF", token_stripped) + return None + + +def _structure_to_anatomy(s: dict[str, Any]) -> models.Anatomy: + return models.Anatomy( + identifier=MBAO_URI_TEMPLATE.format(s["id"]), + name=s["name"], + ) + + +def locations_to_anatomy(locations: list[str]) -> list[models.Anatomy]: + """Convert raw NWB location strings to deduplicated Anatomy list. + + Parameters + ---------- + locations : list[str] + Raw location strings from NWB file. + + Returns + ------- + list[models.Anatomy] + Matched and deduplicated anatomy entries. + """ + seen_ids: set[str] = set() + results: list[models.Anatomy] = [] + for loc in locations: + tokens = _parse_location_string(loc) + for token in tokens: + anatomy = match_location_to_allen(token) + if anatomy is not None: + id_str = str(anatomy.identifier) + if id_str not in seen_ids: + seen_ids.add(id_str) + results.append(anatomy) + return results diff --git a/dandi/metadata/util.py b/dandi/metadata/util.py index 11ccd1a04..090b58aa0 100644 --- a/dandi/metadata/util.py +++ b/dandi/metadata/util.py @@ -516,6 +516,8 @@ def extract_assay_type(metadata: dict) -> list[models.AssayType] | None: def extract_anatomy(metadata: dict) -> list[models.Anatomy] | None: + # Anatomy is now populated via wasDerivedFrom BioSample. + # This extractor is kept only as a fallback for the top-level "anatomy" field. if "anatomy" in metadata: return [models.Anatomy(identifier="anatomy", name=metadata["anatomy"])] else: @@ -552,22 +554,65 @@ def func(metadata: dict) -> list[M]: def extract_wasDerivedFrom(metadata: dict) -> list[models.BioSample] | None: derived_from: list[models.BioSample] | None = None + deepest: models.BioSample | None = None for field, sample_name in [ ("tissue_sample_id", "tissuesample"), ("slice_id", "slice"), ("cell_id", "cell"), ]: if metadata.get(field) is not None: + sample = models.BioSample( + identifier=metadata[field], + wasDerivedFrom=derived_from, + sampleType=models.SampleType(name=sample_name), + ) + derived_from = [sample] + if deepest is None: + deepest = sample + + # Compute anatomy from brain locations (mouse only) + anatomy = _extract_brain_anatomy(metadata) + if anatomy: + if deepest is not None: + # Add anatomy to the deepest (first created) BioSample + deepest.anatomy = anatomy + else: + # No existing chain — create a new BioSample for the anatomy derived_from = [ models.BioSample( - identifier=metadata[field], - wasDerivedFrom=derived_from, - sampleType=models.SampleType(name=sample_name), + identifier="brain-region-sample", + sampleType=models.SampleType(name="tissuesample"), + anatomy=anatomy, ) ] + return derived_from +def _extract_brain_anatomy(metadata: dict) -> list[models.Anatomy]: + """Extract brain anatomy from metadata, if the species is mouse.""" + from .brain_areas import locations_to_anatomy + + locations = metadata.get("brain_locations") + if not locations: + return [] + + # Only apply Allen CCF matching for mouse (NCBITaxon_10090) + species = metadata.get("species") + if species is None: + return [] + species_str = str(species).lower() + is_mouse = ( + "10090" in species_str + or "mus musculus" in species_str + or "mouse" in species_str + ) + if not is_mouse: + return [] + + return locations_to_anatomy(locations) + + extract_wasAttributedTo = extract_model_list( models.Participant, "identifier", "subject_id", id=None ) diff --git a/dandi/pynwb_utils.py b/dandi/pynwb_utils.py index 7ffe552a8..1963e9d73 100644 --- a/dandi/pynwb_utils.py +++ b/dandi/pynwb_utils.py @@ -282,6 +282,9 @@ def _get_pynwb_metadata(path: str | Path | Readable) -> dict[str, Any]: start_time = out["session_start_time"] out["session_end_time"] = start_time + timedelta(seconds=session_duration) + # Extract brain locations for anatomy metadata + out["brain_locations"] = _get_brain_locations(nwb) + return out @@ -384,6 +387,74 @@ def _get_session_duration(nwb: pynwb.NWBFile) -> float | None: return None +def _get_brain_locations(nwb: pynwb.NWBFile) -> list[str]: + """Extract brain location strings from an NWB file. + + Collects location values from imaging planes (ophys), the electrodes + table (ecephys), and intracellular electrodes (icephys). + + Parameters + ---------- + nwb : pynwb.NWBFile + An open NWB file object. + + Returns + ------- + list[str] + Raw location strings found in the file. + """ + locations: list[str] = [] + + # Ophys: imaging planes + for plane in getattr(nwb, "imaging_planes", {}).values(): + loc = getattr(plane, "location", None) + if loc and isinstance(loc, str): + locations.append(loc) + + # Ecephys: electrodes table "location" column + electrodes = getattr(nwb, "electrodes", None) + if electrodes is not None: + try: + col_names = electrodes.colnames + except Exception: + col_names = () + if col_names and "location" in col_names: + try: + locs = electrodes["location"].data[:] + except Exception: + locs = [] + for val in locs: + if isinstance(val, bytes): + val = val.decode("utf-8", errors="replace") + if val and isinstance(val, str): + locations.append(val) + + # Icephys: intracellular electrodes + ic_electrodes = getattr(nwb, "ic_electrodes", None) or getattr( + nwb, "icephys_electrodes", None + ) + if ic_electrodes is not None: + if isinstance(ic_electrodes, dict): + for elec in ic_electrodes.values(): + loc = getattr(elec, "location", None) + if loc and isinstance(loc, str): + locations.append(loc) + else: + # Might be a DynamicTable in some NWB versions + try: + col_names = getattr(ic_electrodes, "colnames", ()) + if col_names and "location" in col_names: + for val in ic_electrodes["location"].data[:]: + if isinstance(val, bytes): + val = val.decode("utf-8", errors="replace") + if val and isinstance(val, str): + locations.append(val) + except Exception: + pass # IC electrode table format varies across NWB versions + + return locations + + def _get_image_series(nwb: pynwb.NWBFile) -> list[dict]: """Retrieves all ImageSeries related metadata from an open nwb file. diff --git a/dandi/tests/test_brain_areas.py b/dandi/tests/test_brain_areas.py new file mode 100644 index 000000000..a21de2aa5 --- /dev/null +++ b/dandi/tests/test_brain_areas.py @@ -0,0 +1,137 @@ +from __future__ import annotations + +import pytest + +from ..metadata.brain_areas import ( + _parse_location_string, + locations_to_anatomy, + match_location_to_allen, +) + + +@pytest.mark.ai_generated +class TestParseLocationString: + def test_simple_acronym(self) -> None: + assert _parse_location_string("VISp") == ["VISp"] + + def test_simple_name(self) -> None: + assert _parse_location_string("Primary visual area") == ["Primary visual area"] + + def test_comma_separated(self) -> None: + assert _parse_location_string("VISp,VISrl,VISlm") == ["VISp", "VISrl", "VISlm"] + + def test_comma_separated_with_spaces(self) -> None: + assert _parse_location_string("VISp, VISrl, VISlm") == [ + "VISp", + "VISrl", + "VISlm", + ] + + def test_dict_literal_with_area(self) -> None: + result = _parse_location_string("{'area': 'VISp', 'depth': '20'}") + assert result == ["VISp"] + + def test_dict_literal_no_area_key(self) -> None: + result = _parse_location_string("{'region_name': 'VISp', 'depth': '20'}") + # Should return non-numeric string values + assert "VISp" in result + + def test_key_value_pairs(self) -> None: + result = _parse_location_string("area: VISp, depth: 175") + assert result == ["VISp"] + + def test_trivial_unknown(self) -> None: + assert _parse_location_string("unknown") == [] + + def test_trivial_none(self) -> None: + assert _parse_location_string("none") == [] + + def test_trivial_na(self) -> None: + assert _parse_location_string("n/a") == [] + + def test_trivial_brain(self) -> None: + assert _parse_location_string("brain") == [] + + def test_empty_string(self) -> None: + assert _parse_location_string("") == [] + + def test_whitespace_only(self) -> None: + assert _parse_location_string(" ") == [] + + def test_comma_list_with_trivial(self) -> None: + result = _parse_location_string("VISp, unknown, CA1") + assert result == ["VISp", "CA1"] + + +@pytest.mark.ai_generated +class TestMatchLocationToAllen: + def test_exact_acronym(self) -> None: + result = match_location_to_allen("VISp") + assert result is not None + assert "MBA_" in str(result.identifier) + assert result.name == "Primary visual area" + + def test_case_insensitive_acronym(self) -> None: + result = match_location_to_allen("visp") + assert result is not None + assert result.name == "Primary visual area" + + def test_exact_name(self) -> None: + result = match_location_to_allen("Primary visual area") + assert result is not None + assert "MBA_" in str(result.identifier) + + def test_case_insensitive_name(self) -> None: + result = match_location_to_allen("primary visual area") + assert result is not None + assert "MBA_" in str(result.identifier) + + def test_no_match(self) -> None: + result = match_location_to_allen("nonexistent_area_xyz") + assert result is None + + def test_empty_string(self) -> None: + result = match_location_to_allen("") + assert result is None + + def test_ca1(self) -> None: + result = match_location_to_allen("CA1") + assert result is not None + assert result.name is not None + assert "CA1" in result.name or "Field CA1" in result.name + + +@pytest.mark.ai_generated +class TestLocationsToAnatomy: + def test_basic(self) -> None: + result = locations_to_anatomy(["VISp"]) + assert len(result) == 1 + assert result[0].name == "Primary visual area" + + def test_deduplication(self) -> None: + result = locations_to_anatomy(["VISp", "VISp", "visp"]) + assert len(result) == 1 + + def test_multiple_locations(self) -> None: + result = locations_to_anatomy(["VISp", "CA1"]) + assert len(result) == 2 + + def test_empty_list(self) -> None: + result = locations_to_anatomy([]) + assert result == [] + + def test_all_unmatched(self) -> None: + result = locations_to_anatomy(["nonexistent_xyz"]) + assert result == [] + + def test_mixed_matched_unmatched(self) -> None: + result = locations_to_anatomy(["VISp", "nonexistent_xyz"]) + assert len(result) == 1 + + def test_trivial_values_filtered(self) -> None: + result = locations_to_anatomy(["unknown", "n/a", "none"]) + assert result == [] + + def test_comma_separated_input(self) -> None: + result = locations_to_anatomy(["VISp,CA1"]) + assert len(result) == 2 diff --git a/dandi/tests/test_metadata.py b/dandi/tests/test_metadata.py index 1d0b8697e..646169c23 100644 --- a/dandi/tests/test_metadata.py +++ b/dandi/tests/test_metadata.py @@ -31,6 +31,7 @@ from hdmf.common import DynamicTable import numpy as np from pydantic import ByteSize +import pynwb from pynwb import NWBHDF5IO, NWBFile, TimeSeries import pytest import requests @@ -75,6 +76,7 @@ def test_get_metadata(simple1_nwb: Path, simple1_nwb_metadata: dict[str, Any]) - # We also populate with nd_types now, although here they would be empty target_metadata["nd_types"] = [] target_metadata["external_file_objects"] = [] + target_metadata["brain_locations"] = [] # we do not populate any subject fields in our simple1_nwb for f in metadata_nwb_subject_fields: target_metadata[f] = None @@ -707,6 +709,131 @@ def test_session_duration_with_events(tmp_path: Path) -> None: assert abs(duration - 157.0) < 1.0 # Allow small floating point errors +@pytest.mark.ai_generated +def test_brain_anatomy_in_wasDerivedFrom(tmp_path: Path) -> None: + """Test that brain anatomy from electrode locations appears in wasDerivedFrom.""" + nwb_path = tmp_path / "test_anatomy.nwb" + session_start = datetime(2020, 1, 1, 12, 0, 0, tzinfo=tzutc()) + + nwbfile = NWBFile( + session_description="test session for anatomy", + identifier="test_anatomy_123", + session_start_time=session_start, + subject=pynwb.file.Subject( + subject_id="mouse001", + species="Mus musculus", + sex="U", + ), + ) + + # Add device and electrode group with a brain location + device = nwbfile.create_device(name="probe0") + electrode_group = nwbfile.create_electrode_group( + name="group0", + description="test electrode group", + location="VISp", + device=device, + ) + nwbfile.add_electrode( + group=electrode_group, + location="VISp", + x=0.0, + y=0.0, + z=0.0, + ) + + with NWBHDF5IO(str(nwb_path), "w") as io: + io.write(nwbfile) + + from ..metadata.nwb import nwb2asset + from ..misctypes import DUMMY_DANDI_ETAG + + asset = nwb2asset(nwb_path, digest=DUMMY_DANDI_ETAG) + assert asset.wasDerivedFrom is not None + assert len(asset.wasDerivedFrom) > 0 + + # Find the deepest BioSample (the one without wasDerivedFrom) + sample = asset.wasDerivedFrom[0] + while sample.wasDerivedFrom: + sample = sample.wasDerivedFrom[0] + + assert sample.anatomy is not None + assert len(sample.anatomy) > 0 + assert "MBA_" in str(sample.anatomy[0].identifier) + assert sample.anatomy[0].name == "Primary visual area" + + +@pytest.mark.ai_generated +def test_brain_anatomy_non_mouse_skipped(tmp_path: Path) -> None: + """Test that brain anatomy is not extracted for non-mouse species.""" + nwb_path = tmp_path / "test_anatomy_rat.nwb" + session_start = datetime(2020, 1, 1, 12, 0, 0, tzinfo=tzutc()) + + nwbfile = NWBFile( + session_description="test session for anatomy", + identifier="test_anatomy_rat_123", + session_start_time=session_start, + subject=pynwb.file.Subject( + subject_id="rat001", + species="Rattus norvegicus", + sex="U", + ), + ) + + device = nwbfile.create_device(name="probe0") + electrode_group = nwbfile.create_electrode_group( + name="group0", + description="test electrode group", + location="VISp", + device=device, + ) + nwbfile.add_electrode( + group=electrode_group, + location="VISp", + x=0.0, + y=0.0, + z=0.0, + ) + + with NWBHDF5IO(str(nwb_path), "w") as io: + io.write(nwbfile) + + from ..metadata.nwb import nwb2asset + from ..misctypes import DUMMY_DANDI_ETAG + + asset = nwb2asset(nwb_path, digest=DUMMY_DANDI_ETAG) + # No wasDerivedFrom should exist (no tissue/slice/cell ids and non-mouse) + assert asset.wasDerivedFrom is None + + +@pytest.mark.ai_generated +def test_brain_anatomy_with_existing_biosample_chain(tmp_path: Path) -> None: + """Test that anatomy is added to the deepest BioSample when chain exists.""" + from ..metadata.util import extract_wasDerivedFrom + + metadata = { + "tissue_sample_id": "tissue01", + "slice_id": "slice01", + "cell_id": "cell01", + "brain_locations": ["VISp", "CA1"], + "species": "Mus musculus", + } + result = extract_wasDerivedFrom(metadata) + assert result is not None + + # Navigate to deepest sample (tissue) + sample = result[0] # cell + assert sample.identifier == "cell01" + assert sample.wasDerivedFrom is not None + sample = sample.wasDerivedFrom[0] # slice + assert sample.identifier == "slice01" + assert sample.wasDerivedFrom is not None + sample = sample.wasDerivedFrom[0] # tissue (deepest) + assert sample.identifier == "tissue01" + assert sample.anatomy is not None + assert len(sample.anatomy) >= 1 + + @mark_xfail_ontobee @mark.skipif_no_network @pytest.mark.obolibrary diff --git a/pyproject.toml b/pyproject.toml index bb1ab9295..e62405bfa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -161,7 +161,7 @@ tag_prefix = "" parentdir_prefix = "" [tool.codespell] -skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml" +skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml,allen_ccf_structures.json" # Don't warn about "[l]ist" in the abbrev_prompt() docstring: # TE is present in the BIDS schema ignore-regex = "(\\[\\w\\]\\w+|TE|ignore \"bu\" strings)" diff --git a/tox.ini b/tox.ini index ffdb9b6e9..cf1e0c062 100644 --- a/tox.ini +++ b/tox.ini @@ -44,6 +44,8 @@ commands = sphinx-build -E -W -b html source build [pytest] addopts = --tb=short --durations=10 --timeout=300 +markers = + ai_generated: marks tests as AI-generated filterwarnings = error ignore:No cached namespaces found .*:UserWarning