Create cvs for allen 2015, 2017, 2022 and WHS v2, v3, v4

Write and run function for correctly formatted label file

annotation_volumes/WHS_v2_colours.csv

+idx,r,g,b,a,VIS,MSH,label
+1,255,52,39,1.0,1.0,0.0,descending corticofugal pathways
+2,255,186,0,1.0,1.0,0.0,substantia nigra
+3,0,0,255,1.0,1.0,0.0,subthalamic nucleus
+4,255,255,0,1.0,1.0,0.0,molecular layer of the cerebellum
+5,0,255,255,1.0,1.0,0.0,granule cell level of the cerebellum
+6,255,0,255,1.0,1.0,0.0,alveus of the hippocampus
+7,52,255,13,1.0,1.0,0.0,inferior cerebellar peduncle
+10,29,104,235,1.0,1.0,0.0,"cingulate cortex, area 2"
+30,129,79,255,1.0,1.0,0.0,striatum
+31,255,145,186,1.0,1.0,0.0,globus pallidus
+32,26,231,255,1.0,1.0,0.0,entopeduncular nucleus
+33,2,44,255,1.0,1.0,0.0,ventricular system
+34,212,255,0,1.0,1.0,0.0,medial lemniscus
+35,0,176,63,1.0,1.0,0.0,facial nerve
+36,124,252,0,1.0,1.0,0.0,"anterior commissure, anterior part"
+37,255,186,0,1.0,1.0,0.0,"anterior commissure, posterior part"
+38,174,0,232,1.0,1.0,0.0,ventral hippocampal commissure
+39,0,100,0,1.0,1.0,0.0,thalamus
+40,255,8,0,1.0,1.0,0.0,septal region
+41,48,218,0,1.0,1.0,0.0,optic nerve
+42,38,126,255,1.0,1.0,0.0,optic tract and optic chiasm
+43,218,170,62,1.0,1.0,0.0,pineal gland
+44,0,165,21,1.0,1.0,0.0,inner ear
+45,134,255,90,0.68,1.0,0.0,spinal cord
+46,33,230,255,1.0,1.0,0.0,commissure of the superior colliculus
+47,153,83,255,1.0,1.0,0.0,brainstem
+48,226,120,161,1.0,1.0,0.0,hypothalamic region
+49,238,47,44,1.0,1.0,0.0,inferior colliculus
+50,86,0,221,1.0,1.0,0.0,superficial gray layer of the superior colliculus
+51,7,255,89,1.0,1.0,0.0,periaqueductal gray
+52,21,192,255,1.0,1.0,0.0,fornix
+53,238,186,0,1.0,1.0,0.0,mammillothalamic tract
+54,173,255,47,1.0,1.0,0.0,commissural stria terminalis
+55,225,151,15,1.0,1.0,0.0,deeper layers of the superior colliculus
+56,235,87,255,1.0,1.0,0.0,periventricular gray
+57,250,244,247,1.0,1.0,0.0,genu of the facial nerve
+58,0,215,11,1.0,1.0,0.0,pontine nuclei
+59,0,255,29,1.0,1.0,0.0,fimbria of the hippocampus
+60,244,67,69,1.0,1.0,0.0,fasciculus retroflexus
+61,255,252,0,1.0,1.0,0.0,stria medullaris of the thalamus
+62,238,117,51,1.0,1.0,0.0,stria terminalis
+63,255,0,218,1.0,1.0,0.0,posterior commissure
+64,15,109,230,1.0,1.0,0.0,glomerular layer of the accessory olfactory bulb
+65,255,227,0,1.0,1.0,0.0,glomerular layer of the olfactory bulb
+66,255,135,0,1.0,1.0,0.0,olfactory bulb
+67,255,110,0,1.0,1.0,0.0,corpus callosum and associated subcortical white matter
+68,188,32,173,1.0,1.0,0.0,brachium of the superior colliculus
+69,147,255,39,1.0,1.0,0.0,commissure of the inferior colliculus
+70,39,244,253,1.0,1.0,0.0,central canal
+71,63,192,255,1.0,1.0,0.0,interpeduncular nucleus
+72,179,28,53,1.0,1.0,0.0,ascending fibers of the facial nerve
+73,255,79,206,1.0,1.0,0.0,anterior commissure
+74,0,246,14,1.0,1.0,0.0,inferior olive
+75,91,241,255,1.0,1.0,0.0,spinal trigeminal nuclus
+76,250,128,114,1.0,1.0,0.0,spinal trigeminal tract
+77,206,211,7,1.0,1.0,0.0,frontal associiation cortex
+78,134,204,76,1.0,1.0,0.0,middle cerebellar peduncle
+79,128,170,255,1.0,1.0,0.0,transverse fibers of the pons
+80,69,235,202,1.0,1.0,0.0,habenular commissure
+81,222,7,237,1.0,1.0,0.0,nucleus of the stria medullaris
+82,225,240,13,1.0,1.0,0.0,basal forebrain region
+83,250,170,64,1.0,1.0,0.0,supraoptic decussation
+84,65,150,255,1.0,1.0,0.0,medial lemniscus decussation
+85,114,9,212,1.0,1.0,0.0,pyramidal decussation
+92,3,193,45,1.0,1.0,0.0,neocortex
+93,0,8,182,1.0,1.0,0.0,bed nucleus of the stria terminalis
+94,255,87,30,1.0,1.0,0.0,pretectal region
+95,165,131,107,1.0,1.0,1.0,cornu ammonis 3
+96,91,45,10,1.0,1.0,1.0,dentate gyrus
+97,255,255,0,1.0,1.0,1.0,cornu ammonis 2
+98,217,104,13,1.0,1.0,1.0,cornu ammonis 1
+99,255,82,82,1.0,1.0,1.0,fasciola cinereum
+100,255,192,0,1.0,1.0,1.0,subiculum
+108,40,112,130,1.0,1.0,1.0,postrhinal cortex
+109,80,123,175,1.0,1.0,1.0,presubiculum
+110,23,54,96,1.0,1.0,1.0,parasubiculum
+112,205,51,255,1.0,1.0,1.0,perirhinal area 35
+113,112,48,160,1.0,1.0,1.0,perirhinal area 36
+114,12,92,8,1.0,1.0,1.0,entorhinal cortex
+115,221,166,36,1.0,1.0,1.0,lateral entorhinal cortex
+0,0,0,0,1.0,1.0,1.0,Clear Label

annotation_volumes/WHS_v3_colours.csv

+idx,r,g,b,a,VIS,MSH,label
+1,255,52,39,1.0,1.0,0.0,descending corticofugal pathways
+2,255,186,0,1.0,1.0,0.0,substantia nigra
+3,0,0,255,1.0,1.0,0.0,subthalamic nucleus
+4,255,255,0,1.0,1.0,0.0,molecular layer of the cerebellum
+5,0,255,255,1.0,1.0,0.0,granule cell level of the cerebellum
+6,255,0,255,1.0,1.0,0.0,alveus of the hippocampus
+7,52,255,13,1.0,1.0,0.0,inferior cerebellar peduncle
+10,29,104,235,1.0,1.0,0.0,"cingulate cortex, area 2"
+30,129,79,255,1.0,1.0,0.0,striatum
+31,255,145,186,1.0,1.0,0.0,globus pallidus
+32,26,231,255,1.0,1.0,0.0,entopeduncular nucleus
+33,2,44,255,1.0,1.0,0.0,ventricular system
+34,212,255,0,1.0,1.0,0.0,medial lemniscus
+35,255,25,240,1.0,1.0,0.0,facial nerve
+36,124,252,0,1.0,1.0,0.0,"anterior commissure, anterior part"
+37,255,186,0,1.0,1.0,0.0,"anterior commissure, posterior part"
+38,174,0,232,1.0,1.0,0.0,ventral hippocampal commissure
+39,0,100,0,1.0,1.0,0.0,thalamus
+40,255,8,0,1.0,1.0,0.0,septal region
+41,48,218,0,1.0,1.0,0.0,optic nerve
+42,38,126,255,1.0,1.0,0.0,optic tract and optic chiasm
+43,218,170,62,1.0,1.0,0.0,pineal gland
+44,255,255,255,1.0,1.0,0.0,"inner ear, erroneous"
+45,134,255,90,1.0,1.0,0.0,spinal cord
+46,33,230,255,1.0,1.0,0.0,commissure of the superior colliculus
+47,153,83,255,1.0,1.0,0.0,brainstem
+48,226,120,161,1.0,1.0,0.0,hypothalamic region
+50,86,0,221,1.0,1.0,0.0,superficial gray layer of the superior colliculus
+51,7,255,89,1.0,1.0,0.0,periaqueductal gray
+52,21,192,255,1.0,1.0,0.0,fornix
+53,238,186,0,1.0,1.0,0.0,mammillothalamic tract
+54,173,255,47,1.0,1.0,0.0,commissural stria terminalis
+55,225,151,15,1.0,1.0,0.0,deeper layers of the superior colliculus
+56,235,87,255,1.0,1.0,0.0,periventricular gray
+57,250,244,247,1.0,1.0,0.0,genu of the facial nerve
+58,0,215,11,1.0,1.0,0.0,pontine nuclei
+59,0,255,29,1.0,1.0,0.0,fimbria of the hippocampus
+60,244,67,69,1.0,1.0,0.0,fasciculus retroflexus
+61,0,255,0,1.0,1.0,0.0,stria medullaris of the thalamus
+62,238,117,51,1.0,1.0,0.0,stria terminalis
+63,255,0,218,1.0,1.0,0.0,posterior commissure
+64,15,109,230,1.0,1.0,0.0,glomerular layer of the accessory olfactory bulb
+65,255,227,0,1.0,1.0,0.0,glomerular layer of the olfactory bulb
+66,255,135,0,1.0,1.0,0.0,olfactory bulb
+67,255,110,0,1.0,1.0,0.0,corpus callosum and associated subcortical white matter
+68,188,32,173,1.0,1.0,0.0,brachium of the superior colliculus
+69,255,42,39,1.0,1.0,1.0,"inferior colliculus, commissure"
+70,39,244,253,1.0,1.0,0.0,central canal
+71,63,192,255,1.0,1.0,0.0,interpeduncular nucleus
+72,179,28,53,1.0,1.0,0.0,ascending fibers of the facial nerve
+73,255,79,206,1.0,1.0,0.0,anterior commissure
+74,0,246,14,1.0,1.0,0.0,inferior olive
+75,91,241,255,1.0,1.0,0.0,spinal trigeminal nucleus
+76,250,128,114,1.0,1.0,0.0,spinal trigeminal tract
+77,206,211,7,1.0,1.0,0.0,frontal association cortex
+78,134,204,76,1.0,1.0,0.0,middle cerebellar peduncle
+79,128,170,255,1.0,1.0,0.0,transverse fibers of the pons
+80,69,235,202,1.0,1.0,0.0,habenular commissure
+81,222,7,237,1.0,1.0,0.0,nucleus of the stria medullaris
+82,225,240,13,1.0,1.0,0.0,basal forebrain region
+83,250,170,64,1.0,1.0,0.0,supraoptic decussation
+84,65,150,255,1.0,1.0,0.0,medial lemniscus decussation
+85,114,9,212,1.0,1.0,0.0,pyramidal decussation
+92,3,193,45,1.0,1.0,0.0,neocortex
+93,0,8,182,1.0,1.0,0.0,bed nucleus of the stria terminalis
+94,255,87,30,1.0,1.0,0.0,pretectal region
+95,165,131,107,1.0,1.0,0.0,cornu ammonis 3
+96,91,45,10,1.0,1.0,0.0,dentate gyrus
+97,255,255,0,1.0,1.0,0.0,cornu ammonis 2
+98,217,104,13,1.0,1.0,0.0,cornu ammonis 1
+99,255,0,0,1.0,1.0,0.0,fasciola cinereum
+100,255,192,0,1.0,1.0,0.0,subiculum
+108,40,112,130,1.0,1.0,0.0,postrhinal cortex
+109,80,123,175,1.0,1.0,0.0,presubiculum
+110,23,54,96,1.0,1.0,0.0,parasubiculum
+112,205,51,255,1.0,1.0,0.0,perirhinal area 35
+113,112,48,160,1.0,1.0,0.0,perirhinal area 36
+114,122,187,51,1.0,1.0,0.0,entorhinal cortex
+115,90,111,47,1.0,1.0,0.0,lateral entorhinal cortex
+119,0,144,55,1.0,1.0,1.0,vestibular apparatus
+120,0,255,29,1.0,1.0,1.0,cochlea
+121,253,148,0,1.0,1.0,1.0,cochlear nerve
+122,253,50,0,1.0,1.0,1.0,vestibular nerve
+123,0,12,255,1.0,1.0,1.0,"ventral cochlear nucleus, granule cell layer"
+125,52,29,144,1.0,1.0,0.0,4th ventricle
+126,92,156,211,1.0,1.0,1.0,"dorsal cochlear nucleus, molecular layer"
+127,0,80,156,1.0,1.0,1.0,"dorsal cochlear nucleus, fusiform and granule layer"
+128,197,238,255,1.0,1.0,1.0,"dorsal cochlear nucleus, deep core"
+129,255,217,0,1.0,1.0,1.0,acoustic striae
+130,213,255,0,1.0,1.0,1.0,trapezoid body
+131,0,255,81,1.0,1.0,1.0,nucleus of the trapezoid body
+132,0,238,255,1.0,1.0,1.0,superior paraolivary nucleus
+133,219,239,61,1.0,1.0,1.0,medial superior olive
+134,35,76,190,1.0,1.0,1.0,lateral superior olive
+135,1,153,21,1.0,1.0,1.0,superior periolivary region
+136,0,174,255,1.0,1.0,1.0,ventral periolivary nuclei
+137,255,0,115,1.0,1.0,1.0,"lateral lemniscus, ventral nucleus"
+138,171,16,91,1.0,1.0,1.0,"lateral lemniscus, intermediate nucleus"
+139,108,18,91,1.0,1.0,1.0,"lateral lemniscus, dorsal nucleus"
+140,255,29,0,1.0,1.0,1.0,"lateral lemniscus, commissure"
+141,255,166,0,1.0,1.0,1.0,lateral lemniscus
+142,206,255,142,1.0,1.0,1.0,"inferior colliculus, dorsal cortex"
+143,0,238,255,1.0,1.0,1.0,"inferior colliculus, central nucleus"
+145,48,136,203,1.0,1.0,1.0,"inferior colliculus, external cortex"
+146,176,58,72,1.0,1.0,1.0,"inferior colliculus, brachium"
+147,10,244,217,1.0,1.0,1.0,"medial geniculate body, medial division"
+148,239,163,0,1.0,1.0,1.0,"medial geniculate body, dorsal division"
+149,131,58,31,1.0,1.0,1.0,"medial geniculate body, ventral division"
+150,255,47,242,1.0,1.0,1.0,"medial geniculate body, marginal zone"
+151,255,215,0,1.0,1.0,1.0,primary auditory cortex
+152,240,255,255,1.0,1.0,1.0,"secondary auditory cortex, dorsal area"
+153,216,191,216,1.0,1.0,1.0,"secondary auditory cortex, ventral area"
+157,244,156,255,1.0,1.0,1.0,auditory radiation
+158,34,152,255,1.0,1.0,1.0,"ventral cochlear nucleus, anterior part"
+159,0,230,207,1.0,1.0,1.0,"ventral cochlear nucleus, posterior part"
+160,0,255,106,1.0,1.0,1.0,"ventral cochlear nucleus, cap area"
+162,185,255,233,1.0,1.0,1.0,spiral ganglion
+163,99,205,0,1.0,1.0,1.0,nucleus sagulum
+164,110,0,255,1.0,1.0,1.0,"reticular thalamic nucleus, auditory segment"
+0,0,0,0,1.0,1.0,1.0,Clear Label

annotation_volumes/WHS_v4_colours.csv

-allenID,r,g,b,1a,1b,1c,name
+idx,r,g,b,a,VIS,MSH,label
 1,255,52,39,1.0,1.0,0.0,corticofugal tract and corona radiata
 3,0,0,255,1.0,1.0,0.0,Subthalamic nucleus
 4,255,255,1,1.0,1.0,0.0,Molecular cell layer of the cerebellum

annotation_volumes/allen2015_colours.csv

-allenID,r,g,b,1a,1b,1c,name
+idx,r,g,b,a,VIS,MSH,label
 997,255,255,255,1.0,1.0,1.0,root
 8,191,218,227,1.0,1.0,1.0,Basic cell groups and regions
 567,176,240,255,1.0,1.0,1.0,Cerebrum

annotation_volumes/allen2017_colours.csv

-allenID,r,g,b,1a,1b,1c,name
+idx,r,g,b,a,VIS,MSH,label
 997,255,255,255,1.0,1.0,1.0,root
 8,191,218,227,1.0,1.0,1.0,Basic cell groups and regions
 567,176,240,255,1.0,1.0,1.0,Cerebrum

scripts/reformat_allen_label.py → scripts/reformat_label_files.py

@@ -2,16 +2,16 @@ import pandas as pd
 
 """reformat itksnap_label_description_2022.txt"""
 def reformat_allen_label(inputpath, outputpath):
-    df = pd.read_csv(inputpath, sep=" ", header=None,  names=["id", "r", "g", "b", "1a", "1b", "1c", "name"])
+    df = pd.read_csv(inputpath, sep=" ", header=None,  names=["id", "r", "g", "b", "a", "VIS", "MSH", "label"])
     
     # this is to reformat the name to allenID
-    df[["name", "allenID"]] = df["name"].str.split(' - ', expand=True)
+    df[["label", "idx"]] = df["label"].str.split(' - ', expand=True)
     
     # this is to add on "root" as this was missing from the Allen file
-    df = df.append({"allenID": 0, "name": "background", "r": 255, "g": 255, "b": 255, "1a": 1.0, "1b":1.0, "1c":1.0}, ignore_index=True)
+    df = df.append({"idx": 0, "label": "background", "r": 255, "g": 255, "b": 255, "a": 1.0, "VIS":1.0, "MSH":1.0}, ignore_index=True)
     df.to_csv(outputpath, index=False)
 
-reformat_allen_label("../junk/itksnap_label_description_2022.txt","../junk/allen2022_colours.csv")
+reformat_allen_label("../junk/itksnap_label_description_2022.txt","../annotation_volumes/allen2022_colours_updated.csv")
 
 
 """reformat AllenMouseBrain_atlas_CCF_2017.label"""