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Commit d9f8a7f1 authored by Sharon Yates's avatar Sharon Yates
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Reformat allen and WHS label files

Write function to reformat label files so they are compatible with PyNutil
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allenID,r,g,b,1a,1b,1c,name
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
5,0,255,255,1.0,1.0,0.0,"Cerebellum, unspecified"
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 area 2
32,26,231,255,1.0,1.0,0.0,Entopeduncular nucleus
33,2,44,255,1.0,1.0,0.0,"Ventricular system, unspecified"
34,212,255,0,1.0,1.0,0.0,"medial lemniscus, unspecified"
35,255,25,240,1.0,1.0,0.0,"facial nerve, unspecified"
36,124,252,0,1.0,1.0,0.0,"anterior commissure, anterior limb"
37,255,186,0,1.0,1.0,0.0,"anterior commissure, posterior limb"
38,174,0,232,1.0,1.0,0.0,ventral hippocampal commissure
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
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, unspecified"
48,226,120,161,1.0,1.0,0.0,"Hypothalamic region, unspecified"
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,mammillotegmental 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 thalami
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, unspecified"
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
69,255,42,39,1.0,1.0,0.0,"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, intrabulbar part"
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, unspecified"
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
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,Medial entorhinal cortex
115,90,111,47,1.0,1.0,0.0,Lateral entorhinal cortex
119,0,144,55,1.0,1.0,0.0,Vestibular apparatus
120,0,255,28,1.0,1.0,0.0,Cochlea
121,253,148,0,1.0,1.0,0.0,Cochlear nerve
122,253,50,0,1.0,1.0,0.0,Vestibular nerve
123,0,12,255,1.0,1.0,0.0,"Ventral cochlear nucleus, granule cell layer"
125,52,29,144,1.0,1.0,0.0,4th ventricle
126,92,156,211,1.0,1.0,0.0,"Dorsal cochlear nucleus, molecular layer"
127,0,80,156,1.0,1.0,0.0,"Dorsal cochlear nucleus, fusiform and granule layer"
128,197,238,255,1.0,1.0,0.0,"Dorsal cochlear nucleus, deep core"
129,255,217,0,1.0,1.0,0.0,acoustic striae
130,213,255,0,1.0,1.0,0.0,trapezoid body
131,0,255,81,1.0,1.0,0.0,Nucleus of the trapezoid body
132,0,238,255,1.0,1.0,0.0,Superior paraolivary nucleus
133,219,239,61,1.0,1.0,0.0,Medial superior olive
134,35,76,190,1.0,1.0,0.0,Lateral superior olive
135,1,153,21,1.0,1.0,0.0,Superior periolivary region
136,0,174,255,1.0,1.0,0.0,Ventral periolivary nuclei
137,255,0,115,1.0,1.0,0.0,"Lateral lemniscus, ventral nucleus"
138,171,16,91,1.0,1.0,0.0,"Lateral lemniscus, intermediate nucleus"
139,108,18,91,1.0,1.0,0.0,"Lateral lemniscus, dorsal nucleus"
140,255,29,0,1.0,1.0,0.0,"lateral lemniscus, commissure"
141,255,166,0,1.0,1.0,0.0,"lateral lemniscus, unspecified"
142,206,255,142,1.0,1.0,0.0,"Inferior colliculus, dorsal cortex"
143,0,238,254,1.0,1.0,0.0,"Inferior colliculus, central nucleus"
145,48,136,203,1.0,1.0,0.0,"Inferior colliculus, external cortex"
146,176,58,72,1.0,1.0,0.0,"inferior colliculus, brachium"
150,255,47,242,1.0,1.0,0.0,"Medial geniculate body, marginal zone"
151,255,215,0,1.0,1.0,0.0,Primary auditory area
152,240,255,255,1.0,1.0,0.0,"Secondary auditory area, dorsal part"
153,216,191,216,1.0,1.0,0.0,"Secondary auditory area, ventral part"
157,244,156,255,1.0,1.0,0.0,"external medullary lamina, auditory radiation"
158,34,152,255,1.0,1.0,0.0,"Ventral cochlear nucleus, anterior part"
159,0,230,207,1.0,1.0,0.0,"Ventral cochlear nucleus, posterior part"
160,0,255,106,1.0,1.0,0.0,"Ventral cochlear nucleus, cap area"
162,185,255,233,1.0,1.0,0.0,Spiral ganglion
163,99,205,0,1.0,1.0,0.0,Nucleus sagulum
164,110,0,255,1.0,1.0,0.0,"Reticular (pre)thalamic nucleus, auditory segment"
180,255,0,221,1.0,1.0,0.0,lateral olfactory tract
181,0,204,255,1.0,1.0,0.0,"Piriform cortex, layer 1"
182,0,0,254,1.0,1.0,0.0,"Piriform cortex, layer 2"
183,165,120,221,1.0,1.0,0.0,"Piriform cortex, layer 3"
184,230,216,250,1.0,1.0,0.0,"Nucleus accumbens, core"
187,99,197,18,1.0,1.0,0.0,"Substantia nigra, reticular part"
188,255,255,127,1.0,1.0,0.0,"Substantia nigra, compact part"
189,0,159,159,1.0,1.0,0.0,"Substantia nigra, lateral part"
192,88,47,108,1.0,1.0,0.0,"Nucleus accumbens, shell"
193,0,162,255,1.0,1.0,0.0,Ventral pallidum
195,255,85,255,1.0,1.0,0.0,"Globus pallidus external, medial part"
196,127,255,212,1.0,1.0,0.0,Ventral tegmental area
197,129,79,155,1.0,1.0,0.0,Caudate putamen
198,200,25,200,1.0,1.0,0.0,"Globus pallidus external, lateral part"
199,220,20,60,1.0,1.0,0.0,"Ventral striatal region, unspecified"
200,0,217,255,1.0,1.0,0.0,"Reticular (pre)thalamic nucleus, unspecified"
201,183,199,136,1.0,1.0,0.0,Peripeduncular nucleus
204,255,25,0,1.0,1.0,0.0,Pregeniculate nucleus
205,255,226,0,1.0,1.0,0.0,Dorsal lateral geniculate nucleus
206,217,108,0,1.0,1.0,0.0,Lateral habenular nucleus
207,205,0,24,1.0,1.0,0.0,Medial habenular nucleus
208,228,112,214,1.0,1.0,0.0,Posterior intralaminar nucleus
210,255,255,200,1.0,1.0,0.0,"Posterior thalamic nuclear group, triangular part"
211,205,0,6,1.0,1.0,0.0,Parataenial thalamic nucleus
213,131,10,121,1.0,1.0,0.0,Anterodorsal thalamic nucleus
214,239,121,218,1.0,1.0,0.0,"Anteroventral thalamic nucleus, dorsomedial part"
215,101,35,142,1.0,1.0,0.0,"Anteroventral thalamic nucleus, ventrolateral part"
216,0,255,17,1.0,1.0,0.0,Rhomboid thalamic nucleus
218,35,255,236,1.0,1.0,0.0,Xiphoid thalamic nucleus
219,255,170,0,1.0,1.0,0.0,Reuniens thalamic nucleus
221,0,185,126,1.0,1.0,0.0,Ventromedial thalamic nucleus
222,130,0,217,1.0,1.0,0.0,Submedius thalamic nucleus
223,139,93,139,1.0,1.0,0.0,Angular thalamic nucleus
227,255,0,254,1.0,1.0,0.0,Ventral posteromedial thalamic nucleus
228,255,123,0,1.0,1.0,0.0,"Laterodorsal thalamic nucleus, dorsomedial part"
229,43,153,31,1.0,1.0,0.0,"Laterodorsal thalamic nucleus, ventrolateral part"
230,255,255,2,1.0,1.0,0.0,Posterior thalamic nucleus
231,170,170,255,1.0,1.0,0.0,Ventrolateral thalamic nucleus
232,255,85,127,1.0,1.0,0.0,"Mediodorsal thalamic nucleus, lateral part"
233,85,170,0,1.0,1.0,0.0,"Mediodorsal thalamic nucleus, central part"
235,216,191,217,1.0,1.0,0.0,"Zona incerta, dorsal part"
236,75,200,138,1.0,1.0,0.0,"Zona incerta, ventral part"
238,194,71,79,1.0,1.0,0.0,"Zona incerta, A13 dopamine cells"
239,219,143,247,1.0,1.0,0.0,pretectothalamic lamina
240,170,255,255,1.0,1.0,0.0,"Mediodorsal thalamic nucleus, medial part"
242,156,51,51,1.0,1.0,0.0,Paraventricular thalamic nuclei (anterior and posterior)
246,240,248,255,1.0,1.0,0.0,Paracentral thalamic nucleus
247,224,182,64,1.0,1.0,0.0,Central medial thalamic nucleus
248,153,50,204,1.0,1.0,0.0,Central lateral thalamic nucleus
249,170,255,0,1.0,1.0,0.0,"external medullary lamina, unspecified"
254,0,85,255,1.0,1.0,0.0,Anteromedial thalamic nucleus
255,248,117,222,1.0,1.0,0.0,Interanteromedial thalamic nucleus
257,30,144,255,1.0,1.0,0.0,"Zona incerta, rostral part"
260,160,82,45,1.0,1.0,0.0,Intermediodorsal thalamic nucleus
266,0,255,8,1.0,1.0,0.0,"Ventral posterior nucleus of the thalamus, parvicellular part"
267,255,239,213,1.0,1.0,0.0,Parafascicular thalamic nucleus
268,0,0,205,1.0,1.0,0.0,Retroreuniens thalamic nucleus
270,210,182,140,1.0,1.0,0.0,superior cerebellar peduncle and prerubral field
272,0,0,128,1.0,1.0,0.0,Intergeniculate leaflet
278,233,150,122,1.0,1.0,0.0,Subparafascicular nucleus
280,255,250,250,1.0,1.0,0.0,Fields of Forel
281,147,112,219,1.0,1.0,0.0,Subgeniculate nucleus
282,131,50,128,1.0,1.0,0.0,Ethmoid-Limitans nucleus
283,199,87,61,1.0,1.0,0.0,"Lateral posterior thalamic nucleus, lateral part"
284,255,182,193,1.0,1.0,0.0,"Zona incerta, A11 dopamine cells"
285,60,179,113,1.0,1.0,0.0,"Lateral posterior thalamic nucleus, mediorostral part"
286,255,235,205,1.0,1.0,0.0,"Lateral posterior thalamic nucleus, mediocaudal part"
287,255,228,196,1.0,1.0,0.0,"Zona incerta, caudal part"
290,155,148,111,1.0,1.0,0.0,intramedullary thalamic area
291,255,92,10,1.0,1.0,0.0,internal medullary lamina
293,255,136,0,1.0,1.0,0.0,Ventral anterior thalamic nucleus
294,171,86,62,1.0,1.0,0.0,Ventral posterolateral thalamic nucleus
295,239,163,0,1.0,1.0,0.0,"Medial geniculate body, dorsal division"
297,10,244,217,1.0,1.0,0.0,"Medial geniculate body, medial division"
298,131,58,31,1.0,1.0,0.0,"Medial geniculate body, ventral division"
299,10,244,150,1.0,1.0,0.0,"Medial geniculate body, suprageniculate nucleus"
400,255,0,1,1.0,1.0,0.0,Ventrolateral orbital area
401,255,174,201,1.0,1.0,0.0,Lateral orbital area
402,200,191,231,1.0,1.0,0.0,Ventral orbital area
403,63,72,204,1.0,1.0,0.0,Medial orbital area
404,185,122,87,1.0,1.0,0.0,Dorsolateral orbital area
405,163,73,164,1.0,1.0,0.0,Prelimbic area
406,0,162,232,1.0,1.0,0.0,Secondary motor area
407,136,0,21,1.0,1.0,0.0,Frontal association area 3
408,153,217,234,1.0,1.0,0.0,Primary motor area
409,255,201,14,1.0,1.0,0.0,"Agranular insular cortex, ventral area"
410,255,127,39,1.0,1.0,0.0,Agranular insular cortex dorsal area
411,0,128,128,1.0,1.0,0.0,Cingulate area 1
412,153,217,200,1.0,1.0,0.0,Claustrum
413,34,177,76,1.0,1.0,0.0,Infralimbic area
414,255,242,0,1.0,1.0,0.0,Dysgranular insular cortex
416,239,228,176,1.0,1.0,0.0,Granular insular cortex
417,185,14,131,1.0,1.0,0.0,"Primary somatosensory area, forelimb representation"
418,237,28,36,1.0,1.0,0.0,"Primary somatosensory area, dysgranular zone"
420,255,128,192,1.0,1.0,0.0,"Primary somatosensory area, face representation"
422,200,100,250,1.0,1.0,0.0,Secondary somatosensory area
423,136,100,21,1.0,1.0,0.0,"Primary somatosensory area, hindlimb representation"
424,181,230,29,1.0,1.0,0.0,"Agranular insular cortex, posterior area "
425,120,177,76,1.0,1.0,0.0,"Primary somatosensory area, barrel field"
427,200,73,164,1.0,1.0,0.0,Retrosplenial dysgranular area
429,225,150,201,1.0,1.0,0.0,"Primary somatosensory area, trunk representation"
430,25,100,200,1.0,1.0,0.0,Retrosplenial granular area
432,255,240,29,1.0,1.0,0.0,"Parietal association cortex, lateral area"
433,108,0,108,1.0,1.0,0.0,"Parietal association cortex, medial area"
436,128,0,64,1.0,1.0,0.0,"Parietal association cortex, posterior area "
442,84,52,35,1.0,1.0,0.0,Primary visual area
443,255,100,100,1.0,1.0,0.0,"Secondary visual area, lateral part"
444,0,128,0,1.0,1.0,0.0,Temporal association cortex
448,128,0,100,1.0,1.0,0.0,"Secondary visual area, medial part"
500,1,10,100,1.0,1.0,0.0,Endopiriform nucleus
501,2,20,200,1.0,1.0,0.0,"Amygdaloid area, unspecified"
502,230,184,67,1.0,1.0,0.0,Nucleus of the lateral olfactory tract
0,0,0,0,1.0,1.0,1.0,Clear Label
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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"])
##for reading gergely format labels try the skiprows argument (might be mispelt sorry). check the
##read csv documentation for more details.
# this is to reformat the name to allenID
df[["name", "allenID"]] = df["name"].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}, ignore_index=True)
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.to_csv(outputpath, index=False)
reformat_allen_label("../junk/itksnap_label_description_2022.txt","../junk/allen2022_colours.csv")
"""Task: Modify the function to reformat Gergely's label files"""
"""reformat AllenMouseBrain_atlas_CCF_2017.label"""
def reformat_label(inputpath, outputpath):
df = pd.read_csv(inputpath, sep = " ", header=None)
df = pd.read_csv(inputpath, sep = "\t", header=None, skiprows=15 ,names=["allenID", "r", "g", "b", "1a", "1b", "1c", "name"] )
df = df.append({"allenID": 0, "name": "Clear Label", "r": 0, "g": 0, "b": 0, "1a": 1.0, "1b":1.0, "1c":1.0}, ignore_index=True)
df.to_csv(outputpath, index=False)
reformat_label("../annotation_volumes/AllenMouseBrain_Atlas_CCF_2017.label","../annotation_volumes/allen2017_colours.csv")
"""reformat AllenMouseBrain_atlas_CCF_2015.label"""
def reformat_label(inputpath, outputpath):
df = pd.read_csv(inputpath, sep = "\t", header=None, skiprows=15 ,names=["allenID", "r", "g", "b", "1a", "1b", "1c", "name"] )
df = df.append({"allenID": 0, "name": "Clear Label", "r": 0, "g": 0, "b": 0, "1a": 1.0, "1b":1.0, "1c":1.0}, ignore_index=True)
df.to_csv(outputpath, index=False)
reformat_label("../annotation_volumes/AllenMouseBrain_Atlas_CCF_2015.label","../annotation_volumes/allen2015_colours.csv")
"""reformat WHS_SD_rat_atlas_v4"""
def reformat_WHS_label(inputpath, outputpath):
df = pd.read_csv(inputpath, sep = "\s+", header=None, skiprows=15 ,names=["allenID", "r", "g", "b", "1a", "1b", "1c", "name"] )
df = df.append({"allenID": 0, "name": "Clear Label", "r": 0, "g": 0, "b": 0, "1a": 1.0, "1b":1.0, "1c":1.0}, ignore_index=True)
df.to_csv(outputpath, index=False)
reformat_WHS_label("../annotation_volumes/WHS_SD_rat_atlas_v4.label","../annotation_volumes/WHS_v4_colours.csv")
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