siibra 1.0a1__1-py3-none-any.whl

siibra/vocabularies/receptor_symbols.json

@@ -0,0 +1,210 @@
+{
+    "5-HT1A": {
+        "receptor": {
+            "latex": "$5-HT_{1A}$",
+            "markdown": "5-HT<sub>1A</sub>",
+            "name": "5-hydroxytryptamine receptor type 1A"
+        },
+        "neurotransmitter": {
+            "label": "5-HT",
+            "latex": "$5-HT$",
+            "markdown": "5-HT",
+            "name": "serotonin"
+        }
+    },
+    "5-HT2": {
+        "receptor": {
+            "latex": "$5-HT_2$",
+            "markdown": "5-HT<sub>2</sub>",
+            "name": "5-hydroxytryptamine receptor type 2"
+        },
+        "neurotransmitter": {
+            "label": "5-HT",
+            "latex": "$5-HT$",
+            "markdown": "5-HT",
+            "name": "serotonin"
+        }
+    },
+    "AMPA": {
+        "receptor": {
+            "latex": "$AMPA$",
+            "markdown": "AMPA",
+            "name": "alpha-amino-3hydroxy-5-methyl-4isoxazolepropionic acid receptor"
+        },
+        "neurotransmitter": {
+            "label": "Glu",
+            "latex": "$Glu$",
+            "markdown": "Glu",
+            "name": "glutamate"
+        }
+    },
+    "BZ": {
+        "receptor": {
+            "latex": "$GABA_A/BZ$",
+            "markdown": "GABA<sub>A</sub>/BZ",
+            "name": "gamma-aminobutyric acid receptor type A / benzodiazepine associated binding site"
+        },
+        "neurotransmitter": {
+            "label": "GABA",
+            "latex": "$GABA$",
+            "markdown": "GABA",
+            "name": "gamma-aminobutyric acid"
+        }
+    },
+    "D1": {
+        "receptor": {
+            "latex": "$D_1$",
+            "markdown": "D<sub>1</sub>",
+            "name": "dopamine receptor type 1"
+        },
+        "neurotransmitter": {
+            "label": "DA",
+            "latex": "$DA$",
+            "markdown": "DA",
+            "name": "dopamine"
+        }
+    },
+    "GABAA": {
+        "receptor": {
+            "latex": "$GABA_A$",
+            "markdown": "GABA<sub>A</sub>",
+            "name": "gamma-aminobutyric acid receptor type A"
+        },
+        "neurotransmitter": {
+            "label": "GABA",
+            "latex": "$GABA$",
+            "markdown": "GABA",
+            "name": "gamma-aminobutyric acid"
+        }
+    },
+    "GABAB": {
+        "receptor": {
+            "latex": "$GABA_B$",
+            "markdown": "GABA<sub>B</sub>",
+            "name": "gamma-aminobutyric acid receptor type B"
+        },
+        "neurotransmitter": {
+            "label": "GABA",
+            "latex": "$GABA$",
+            "markdown": "GABA",
+            "name": "gamma-aminobutyric acid"
+        }
+    },
+    "M1": {
+        "receptor": {
+            "latex": "$M_1$",
+            "markdown": "M<sub>1</sub>",
+            "name": "muscarinic acetylcholine receptor type 1"
+        },
+        "neurotransmitter": {
+            "label": "ACh",
+            "latex": "$ACh$",
+            "markdown": "ACh",
+            "name": "acetylcholine"
+        }
+    },
+    "M2": {
+        "receptor": {
+            "latex": "$M_2$",
+            "markdown": "M<sub>2</sub>",
+            "name": "muscarinic acetylcholine receptor type 2"
+        },
+        "neurotransmitter": {
+            "label": "ACh",
+            "latex": "$ACh$",
+            "markdown": "ACh",
+            "name": "acetylcholine"
+        }
+    },
+    "M3": {
+        "receptor": {
+            "latex": "$M_3$",
+            "markdown": "M<sub>3</sub>",
+            "name": "muscarinic acetylcholine receptor type 3"
+        },
+        "neurotransmitter": {
+            "label": "ACh",
+            "latex": "$ACh$",
+            "markdown": "ACh",
+            "name": "acetylcholine"
+        }
+    },
+    "NMDA": {
+        "receptor": {
+            "latex": "$NMDA$",
+            "markdown": "NMDA",
+            "name": "N-methyl-D-aspartate receptor"
+        },
+        "neurotransmitter": {
+            "label": "Glu",
+            "latex": "$Glu$",
+            "markdown": "Glu",
+            "name": "glutamate"
+        }
+    },
+    "alpha1": {
+        "receptor": {
+            "latex": "$\\alpha_1$",
+            "markdown": "&#945<sub>1</sub>",
+            "name": "alpha-1 adrenergic receptor"
+        },
+        "neurotransmitter": {
+            "label": "NE",
+            "latex": "$NE$",
+            "markdown": "NE",
+            "name": "norepinephrine"
+        }
+    },
+    "alpha2": {
+        "receptor": {
+            "latex": "$\\alpha_2$",
+            "markdown": "&#945<sub>2</sub>",
+            "name": "alpha-2 adrenergic receptor"
+        },
+        "neurotransmitter": {
+            "label": "NE",
+            "latex": "$NE$",
+            "markdown": "NE",
+            "name": "norepinephrine"
+        }
+    },
+    "alpha4beta2": {
+        "receptor": {
+            "latex": "$\\alpha_4\\beta_2$",
+            "markdown": "&#945<sub>4</sub>&#946<sub>2</sub>",
+            "name": "alpha-4 beta-2 nicotinic receptor"
+        },
+        "neurotransmitter": {
+            "label": "ACh",
+            "latex": "$ACh$",
+            "markdown": "ACh",
+            "name": "acetylcholine"
+        }
+    },
+    "kainate": {
+        "receptor": {
+            "latex": "$kainate$",
+            "markdown": "kainate",
+            "name": "kainate receptors"
+        },
+        "neurotransmitter": {
+            "label": "Glu",
+            "latex": "$Glu$",
+            "markdown": "Glu",
+            "name": "glutamate"
+        }
+    },
+    "mGluR2_3": {
+        "receptor": {
+            "latex": "$mGluR2/3$",
+            "markdown": "mGluR2/3",
+            "name": "metabotropic glutamate receptor type 2 and 3"
+        },
+        "neurotransmitter": {
+            "label": "Glu",
+            "latex": "$Glu$",
+            "markdown": "Glu",
+            "name": "glutamate"
+        }
+    }
+}

siibra/vocabularies/region_aliases.json

@@ -0,0 +1,460 @@
+{
+	"Homo sapiens": {
+		"Supramarginal (SM)": {
+			"Homo sapiens": {
+				"mesial precentral gyrus": "exact"
+			}
+		},
+		"hMT+/V5": {
+			"Homo sapiens": {
+				"Area hOc5 (LOC)": "exact"
+			}
+		},
+		"Visual Area v3": {
+			"Homo sapiens": {
+				"Area hOc3v (LingG)": "contains",
+				"Area hOc3d (Cuneus)": "contains"
+			}
+		},
+		"CA (Hippocampus)": {
+			"Homo sapiens": {
+				"CA1": "contains",
+				"CA2": "contains",
+				"CA3": "contains"
+			}
+		},
+		"Frontal Neocortex": {
+			"Homo sapiens": {
+				"frontal lobe": "exact"
+			}
+		},
+		"Inferior Temporal (IT)": {
+			"Homo sapiens": {
+				"Temporal lobe": "contained"
+			}
+		},
+		"Temporal cortex": {
+			"Homo sapiens": {
+				"Temporal lobe": "approximate"
+			}
+		},
+		"Inferior Parietal (IP)": {
+			"Homo sapiens": {
+				"Inferior Parietal Lobule": "contained"
+			}
+		},
+		"Rostral Anterior Cingulate (RAC)": {
+			"Homo sapiens": {
+				"Cingulate gyrus frontal part": "approximate"
+			}
+		},
+		"Transverse Temporal (TT)": {
+			"Homo sapiens": {
+				"Temporal lobe": "contained"
+			}
+		},
+		"Putamen": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Posterior segment of the  arcuate fasciculus": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Area i29 (retrosplenial)": {
+			"Homo sapiens": {
+				"limbic lobe": "contained"
+			}
+		},
+		"temporal cingulate fibres": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"human occipetal area 1": {
+			"Homo sapiens": {
+				"Area hOc1 (V1, 17, CalcS)": "exact"
+			}
+		},
+		"PreS (Subiculum)": {
+			"Homo sapiens": {
+				"HC-Subiculum (Hippocampus)": "contained"
+			}
+		},
+		"medial temporal lobe": {
+			"Homo sapiens": {
+				"Temporal Lobe": "contained"
+			}
+		},
+		"Area 47": {
+			"Homo sapiens": {
+				"Lateral Orbitofrontal": "approximate"
+			}
+		},
+		"Insula (Ins)": {
+			"Homo sapiens": {
+				"Insula": "exact"
+			}
+		},
+		"TrS (Transsubiculum)": {
+			"Homo sapiens": {
+				"HC-Transsubiculum (Hippocampus)": "exact"
+			}
+		},
+		"Direct segment of the  arcuate fasciculus": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"primary visual cortex": {
+			"Homo sapiens": {
+				"Area hOc1 (V1, 17, CalcS)": "exact"
+			}
+		},
+		"primary visual cortex (V1)": {
+			"Homo sapiens": {
+				"Area hOc1 (V1, 17, CalcS)": "exact"
+			}
+		},
+		"short cingulate fibres": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Cingulate Neocortex": {
+			"Homo sapiens": {
+				"Limbic lobe": "contained"
+			}
+		},
+		"Lateral Occipital (LO)": {
+			"Homo sapiens": {
+				"Lateral Occipital Cortex": "exact"
+			}
+		},
+		"Pars Orbitalis (Or)": {
+			"Homo sapiens": {
+				"Frontal Operculum": "approximate"
+			}
+		},
+		"inferior fronto-occipital fasciculus": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"ProS (Subiculum)": {
+			"Homo sapiens": {
+				"HC-Subiculum (Hippocampus)": "contained"
+			}
+		},
+		"Superior Temporal (ST)": {
+			"Homo sapiens": {
+				"STS1": "contains",
+				"STS2": "contains"
+			}
+		},
+		"Superior Parietal (SP)": {
+			"Homo sapiens": {
+				"Superior Parietal Lobule": "close"
+			}
+		},
+		"Precuneus (PrCu)": {
+			"Homo sapiens": {
+				"Parietal Lobe": "approximate"
+			}
+		},
+		"Anterior segment of the  arcuate fasciculus": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Pars Opercularis (Op)": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Posterior Cingulate (PoCi)": {
+			"Homo sapiens": {
+				"Limbic lobe": "contained"
+			}
+		},
+		"Area 9": {
+			"Homo sapiens": {
+				"Frontal lobe": "contained"
+			}
+		},
+		"fornix": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"inferior longitudinal fasciculus": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Middle Temporal (MT)": {
+			"Homo sapiens": {
+				"Temporal lobe": "contained"
+			}
+		},
+		"Caudal Middle Frontal (CMF)": {
+			"Homo sapiens": {
+				"Frontal lobe": "contained"
+			}
+		},
+		"Rostral Middle Frontal (RMF)": {
+			"Homo sapiens": {
+				"Frontal lobe": "contained"
+			}
+		},
+		"anterior Thalamic nucleus": {
+			"Homo sapiens": {
+				"Thalamus": "contained"
+			}
+		},
+		"anterior insular cortex": {
+			"Homo sapiens": {
+				"Insula": "contained"
+			}
+		},
+		"Superior Frontal (SF)": {
+			"Homo sapiens": {
+				"Frontal lobe": "contained"
+			}
+		},
+		"Fusiform (Fu)": {
+			"Homo sapiens": {
+				"Fusiform Gyrus": "exact"
+			}
+		},
+		"FD (DG)": {
+			"Homo sapiens": {
+				"DG (Hippocampus)": "contained"
+			}
+		},
+		"long cingulate fibres": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"Prefrontal cortex": {
+			"Homo sapiens": {
+				"Frontal lobe": "approximate"
+			}
+		},
+		"medial parietal cortex": {
+			"Homo sapiens": {
+				"Parietal lobe": "approximate"
+			}
+		},
+		"Cuneus (Cu)": {
+			"Homo sapiens": {
+				"hOc4d": "contains",
+				"hOc3d": "contains"
+			}
+		},
+		"corticospinal tract": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"somatosensory cortex": {
+			"Homo sapiens": {
+				"Area 3a (PostCG)": "contains",
+				"Area 3b (PostCG)": "contains"
+			}
+		},
+		"Whole brain": {
+			"Homo sapiens": {
+				"Julich-brain": "exact"
+			}
+		},
+		"Isthmus Cingulate (IC)": {
+			"Homo sapiens": {
+				"Limbic lobe": "contained"
+			}
+		},
+		"Auditory Cortex": {
+			"Homo sapiens": {
+				"Superior temporal gyrus": "approximate"
+			}
+		},
+		"Postcetnral (PoC)": {
+			"Homo sapiens": {
+				"postcentral gyrus": "close"
+			}
+		},
+		"Sub (Subiculum)": {
+			"Homo sapiens": {
+				"HC-Subiculum (Hippocampus)": "exact"
+			}
+		},
+		"Pars Triangularis (Tr)": {
+			"Homo sapiens": {
+				"Frontal lobe": "approximate"
+			}
+		},
+		"Postcentral (PoC)": {
+			"Homo sapiens": {
+				"Postcentral gyrus": "exact"
+			}
+		},
+		"Middle Orbitofrontal (MOF)": {
+			"Homo sapiens": {
+				"Medial orbitofrontal cortex": "exact"
+			}
+		},
+		"dorsal anterior cingulate cortex": {
+			"Homo sapiens": {
+				"Limbic lobe": "contained"
+			}
+		},
+		"Temporal Neocortex": {
+			"Homo sapiens": {
+				"Temporal lobe": "approximate"
+			}
+		},
+		"Motor cortex": {
+			"Homo sapiens": {
+				"Area 4a (PreCG)": "contains",
+				"Area 4p (PreCG)": "contains"
+			}
+		},
+		"Superior Parietal  (SP)": {
+			"Homo sapiens": {
+				"Superior parietal lobule": "exact"
+			}
+		},
+		"Caudal Anterior Cingulate (CAC)": {
+			"Homo sapiens": {
+				"cingulate gyrus": "approximate",
+				"frontal part": "approximate"
+			}
+		},
+		"human occipetal area 2": {
+			"Homo sapiens": {
+				"Area hOc2 (V2, 18)": "exact"
+			}
+		},
+		"Lingual (Li)": {
+			"Homo sapiens": {
+				"Occipital cortex": "approximate"
+			}
+		},
+		"Visual Cortex": {
+			"Homo sapiens": {
+				"Occipital cortex": "approximate"
+			}
+		},
+		"Dentate Gyrus": {
+			"Homo sapiens": {
+				"DG (Hippocampus)": "exact"
+			}
+		},
+		"Corpus geniculatum laterale (CGL, LGB, metathalamus)": {
+			"Homo sapiens": {
+				"CGL (Metathalamus)": "exact"
+			}
+		},
+		"human occipetal area 3": {
+			"Homo sapiens": {
+				"Area hOc3v (LingG)": "contains",
+				"Area hOc3d (Cuneus)": "contains"
+			}
+		},
+		"uncinate fasciculus": {
+			"Homo sapiens": {
+				"None": "exact"
+			}
+		},
+		"CA4 (DG)": {
+			"Homo sapiens": {
+				"DG (Hippocampus)": "contains"
+			}
+		},
+		"Area a30 (retrosplenial)": {
+			"Homo sapiens": {
+				"Limbic lobe": "contained"
+			}
+		},
+		"anterior temporal cortex": {
+			"Homo sapiens": {
+				"Temporal lobe": "contained"
+			}
+		},
+		"Supramarginal (SP)": {
+			"Homo sapiens": {
+				"Mesial precentral gyrus": "?"
+			}
+		},
+		"Precentral (PrC)": {
+			"Homo sapiens": {
+				"Precentral gyrus": "close"
+			}
+		},
+		"Mediodorsal Thalamic Nucleus": {
+			"Homo sapiens": {
+				"Thalamus": "contained"
+			}
+		},
+		"Brodmann area 21": {
+			"Homo sapiens": {
+				"Temporal lobe": "contained"
+			}
+		},
+		"Corpus geniculatum mediale (CGM, MGB, metathalamus)": {
+			"Homo sapiens": {
+				"CGM (Metathalamus)": "exact"
+			}
+		},
+		"Visual cortex area 17": {
+			"Homo sapiens": {
+				"Area hOc1 (V1, 17, CalcS)": "exact"
+			}
+		},
+		"Area 46": {
+			"Homo sapiens": {
+				"Frontal lobe": "contained"
+			}
+		},
+		"Lateral Orbitofrontal (LOF)": {
+			"Homo sapiens": {
+				"Lateral orbitofrontal cortex": "exact"
+			}
+		},
+		"superior occipital cortex": {
+			"Homo sapiens": {
+				"Occipital cortex": "contained"
+			}
+		},
+		"Area a29 (retrosplenial)": {
+			"Homo sapiens": {
+				"Limbic lobe": "contained"
+			}
+		},
+		"PaS (Subiculum)": {
+			"Homo sapiens": {
+				"HC-Subiculum (Hippocampus)": "exact"
+			}
+		},
+		"Area Ia (Insula)": {
+			"Homo sapiens": {
+				"Area Ia1 (Insula)": "exact"
+			}
+		},
+		"medial temporal cortex": {
+			"Homo sapiens": {
+				"Temporal lobe": "contained"
+			}
+		}
+	},
+	"Macaca fascicularis": {
+		"pallidum": {
+			"Macaca fascicularis": {
+				"globus pallidus": "exact"
+			}
+		}
+	}
+}

siibra/volumes/__init__.py

@@ -0,0 +1,23 @@
+# Copyright 2018-2024
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Package handling variety of volumes and volume operations"""
+
+from .parcellationmap import Map
+from .providers import provider
+from .volume import from_array, from_file, from_pointcloud, from_nifti, Volume
+
+from ..commons import logger
+from typing import List, Union
+import numpy as np