diff --git a/exc_cell_splitting/README b/exc_cell_splitting/README deleted file mode 100644 index abe8c42..0000000 --- a/exc_cell_splitting/README +++ /dev/null @@ -1,4 +0,0 @@ -This directory contains code to split SSCX excitatory types into subtypes. - -Author: Daniel Keller -Date: October 23, 2022 \ No newline at end of file diff --git a/exc_cell_splitting/hierarchy.json b/exc_cell_splitting/hierarchy.json deleted file mode 100644 index c50cf42..0000000 --- a/exc_cell_splitting/hierarchy.json +++ /dev/null @@ -1,18982 +0,0 @@ -{ - "success": true, - "id": 0, - "start_row": 0, - "num_rows": 1, - "total_rows": 1, - "msg": [ - { - "id": 997, - "atlas_id": -1, - "ontology_id": 1, - "acronym": "root", - "name": "root", - "color_hex_triplet": "FFFFFF", - "graph_order": 0, - "st_level": 0, - "hemisphere_id": 3, - "parent_structure_id": null, - "children": [ - { - "id": 8, - "atlas_id": 0, - "ontology_id": 1, - "acronym": "grey", - "name": "Basic cell groups and regions", - "color_hex_triplet": "BFDAE3", - 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"acronym": "AQ", - "name": "cerebral aqueduct", - "color_hex_triplet": "AAAAAA", - "graph_order": 1300, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 73, - "children": [] - }, - { - "id": 145, - "atlas_id": 725, - "ontology_id": 1, - "acronym": "V4", - "name": "fourth ventricle", - "color_hex_triplet": "AAAAAA", - "graph_order": 1301, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 73, - "children": [ - { - "id": 153, - "atlas_id": 726, - "ontology_id": 1, - "acronym": "V4r", - "name": "lateral recess", - "color_hex_triplet": "AAAAAA", - "graph_order": 1302, - "st_level": 9, - "hemisphere_id": 3, - "parent_structure_id": 145, - "children": [] - } - ] - }, - { - "id": 164, - "atlas_id": 727, - "ontology_id": 1, - "acronym": "c", - "name": "central canal, spinal cord/medulla", - "color_hex_triplet": "AAAAAA", - "graph_order": 1303, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 73, - "children": [] - } - ] - }, - { - "id": 1024, - "atlas_id": 693, - "ontology_id": 1, - "acronym": "grv", - "name": "grooves", - "color_hex_triplet": "AAAAAA", - "graph_order": 1304, - "st_level": 1, - "hemisphere_id": 3, - "parent_structure_id": 997, - "children": [ - { - "id": 1032, - "atlas_id": 694, - "ontology_id": 1, - "acronym": "grv of CTX", - "name": "grooves of the cerebral cortex", - "color_hex_triplet": "AAAAAA", - "graph_order": 1305, - "st_level": 7, - "hemisphere_id": 3, - "parent_structure_id": 1024, - "children": [ - { - "id": 1055, - "atlas_id": 697, - "ontology_id": 1, - "acronym": "eg", - "name": "endorhinal groove", - "color_hex_triplet": "AAAAAA", - "graph_order": 1306, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1032, - "children": [] - }, - { - "id": 1063, - "atlas_id": 698, - "ontology_id": 1, - "acronym": "hf", - "name": "hippocampal fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1307, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1032, - "children": [] - }, - { - "id": 1071, - "atlas_id": 699, - "ontology_id": 1, - "acronym": "rf", - "name": "rhinal fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1308, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1032, - "children": [] - }, - { - "id": 1078, - "atlas_id": 700, - "ontology_id": 1, - "acronym": "ri", - "name": "rhinal incisure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1309, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1032, - "children": [] - } - ] - }, - { - "id": 1040, - "atlas_id": 695, - "ontology_id": 1, - "acronym": "grv of CBX", - "name": "grooves of the cerebellar cortex", - "color_hex_triplet": "AAAAAA", - "graph_order": 1310, - "st_level": 7, - "hemisphere_id": 3, - "parent_structure_id": 1024, - "children": [ - { - "id": 1087, - "atlas_id": 701, - "ontology_id": 1, - "acronym": "pce", - "name": "precentral fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1311, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 1095, - "atlas_id": 702, - "ontology_id": 1, - "acronym": "pcf", - "name": "preculminate fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1312, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 1103, - "atlas_id": 703, - "ontology_id": 1, - "acronym": "pri", - "name": "primary fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1313, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 1112, - "atlas_id": 704, - "ontology_id": 1, - "acronym": "psf", - "name": "posterior superior fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1314, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 1119, - "atlas_id": 705, - "ontology_id": 1, - "acronym": "ppf", - "name": "prepyramidal fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1315, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 3, - "atlas_id": 707, - "ontology_id": 1, - "acronym": "sec", - "name": "secondary fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1316, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 11, - "atlas_id": 708, - "ontology_id": 1, - "acronym": "plf", - "name": "posterolateral fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1317, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 18, - "atlas_id": 709, - "ontology_id": 1, - "acronym": "nf", - "name": "nodular fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1318, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 25, - "atlas_id": 710, - "ontology_id": 1, - "acronym": "sif", - "name": "simple fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1319, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 34, - "atlas_id": 711, - "ontology_id": 1, - "acronym": "icf", - "name": "intercrural fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1320, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 43, - "atlas_id": 712, - "ontology_id": 1, - "acronym": "apf", - "name": "ansoparamedian fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1321, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 49, - "atlas_id": 713, - "ontology_id": 1, - "acronym": "ipf", - "name": "intraparafloccular fissure", - "color_hex_triplet": "AAAAAA", - "graph_order": 1322, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 57, - "atlas_id": 714, - "ontology_id": 1, - "acronym": "pms", - "name": "paramedian sulcus", - "color_hex_triplet": "AAAAAA", - "graph_order": 1323, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - }, - { - "id": 65, - "atlas_id": 715, - "ontology_id": 1, - "acronym": "pfs", - "name": "parafloccular sulcus", - "color_hex_triplet": "AAAAAA", - "graph_order": 1324, - "st_level": 8, - "hemisphere_id": 3, - "parent_structure_id": 1040, - "children": [] - } - ] - }, - { - "id": 624, - "atlas_id": 926, - "ontology_id": 1, - "acronym": "IPF", - "name": "Interpeduncular fossa", - "color_hex_triplet": "AAAAAA", - "graph_order": 1325, - "st_level": 7, - "hemisphere_id": 3, - "parent_structure_id": 1024, - "children": [] - } - ] - }, - { - "id": 304325711, - "atlas_id": null, - "ontology_id": 1, - "acronym": "retina", - "name": "retina", - "color_hex_triplet": "7F2E7E", - "graph_order": 1326, - "st_level": 1, - "hemisphere_id": 3, - "parent_structure_id": 997, - "children": [] - } - ] - } - ] -} \ No newline at end of file diff --git a/exc_cell_splitting/make_new_inhib_exc_outside_SSCX.py b/exc_cell_splitting/make_new_inhib_exc_outside_SSCX.py deleted file mode 100644 index 65b59be..0000000 --- a/exc_cell_splitting/make_new_inhib_exc_outside_SSCX.py +++ /dev/null @@ -1,109 +0,0 @@ - -############################################################################### -# Copyright 2022 Blue Brain -# Author: Daniel Keller -# October 21, 2022 -# This program makes exc and inh densities with SSCX cut out -# It also remaps exc cells to morphological fractions in those regions -# using the m-type fractions in the cxv file. All etype exc types are the same. - -# inputs: annoation atlas and hirearchy -# total neuron and inhibitory nrrd files -# mapping csv file -# outputs: (in output directory) -# exc and inhib densities without SSCX -# ME type excitatory nrrd files -############################################################################### - -#packages -import os -import re -from voxcell import VoxelData -from voxcell.nexus.voxelbrain import Atlas -import numpy as np - -#load an nrrd -def find_regions(fn_cand, root, format="path"): - #for fn_cand in fn_regions: - if 1: - expected_fn_regions = os.path.join(root, fn_cand) - if os.path.isfile(expected_fn_regions): - if format == "path": - return expected_fn_regions - elif format == "voxcell": - return VoxelData.load_nrrd(expected_fn_regions) - raise ValueError("Unknown format spec: {0}".format(format)) - return None - - -#make excitatory density -neuron_nrrd= find_regions("neuron_density_v3.nrrd",'./', "voxcell") -inh_nrrd= find_regions("gad67+_density_v3.nrrd",'./', "voxcell") -exc_nrrd=neuron_nrrd -exc_nrrd.raw=neuron_nrrd.raw-inh_nrrd.raw -exc_nrrd.raw=exc_nrrd.raw*(exc_nrrd.raw>0) - -#Do remapping - -#read in mapping file -import csv -allrows=[] -with open('mapping_cortex_all_to_exc_mtypes.csv', newline='') as csvfile: - reader = csv.reader(csvfile, delimiter=',', quotechar='|') - for row in reader: - allrows.append(row) - #print(', '.join(row)) - - -#load atlas -atlas = Atlas.open('.') -brain_regions = atlas.load_data('brain_regions') - - -#make output directory -if (os.path.exists('./output')): - print('output directory already exists') -else: - os.mkdir('output') - - -output_brain_regions=atlas.load_data('brain_regions') -PC_morphology_names=allrows[0] - -#layer IDs, starting with layer 2 and going to layer 6 -allids=[{614454286,614454294,614454296,614454298,614454300,614454302,614454304,614454306},{614454287,614454289,614454291,614454293,614454295,614454297,614454299,614454301,614454303,614454305,614454307},{12995,865,654,1047,1094,950,577,1086,182305701,1035}, {12996,921,702,1070,1128,974,625,1111,182305705,1090}, {12997,12998,686,719,889,929,1038,1062,478,510,1102,2,945,1026,9,461,182305709,182305713,862,893}] - -#loop through the layers and write out ME fractions of PCs in those layers -for count1 in range(1,len(allrows)): - print(count1) - ids=allids[count1-1] - - row=allrows[count1] - region_inds=np.transpose(np.nonzero(np.isin(brain_regions.raw, list(ids)))) - for count2 in range(1,len(PC_morphology_names)): - if row[count2]=='0': - continue - scale=float(row[count2]) - output_name='./output/'+(PC_morphology_names[count2])+'_cADpyr.nrrd' - output_array=0*exc_nrrd.raw - allval=0 - for ind in region_inds: - val=exc_nrrd.raw[ind[0],ind[1],ind[2]] - output_array[ind[0],ind[1],ind[2]]=scale*val - allval+=val - - output_brain_regions.raw=output_array - output_brain_regions.save_nrrd(output_name) - -#now remove regions from excitatory -#append layer 1 -allids.append({12993,793,558,981,480149206,1030,878,450,1006,182305693,873 }) -for ids in allids: - region_inds=np.transpose(np.nonzero(np.isin(brain_regions.raw, list(ids)))) - for ind in region_inds: - exc_nrrd.raw[ind[0],ind[1],ind[2]]=0 - inh_nrrd.raw[ind[0],ind[1],ind[2]]=0 - -#save the output -exc_nrrd.save_nrrd('./output/Generic_Excitatory_Neuron_MType_Generic_Excitatory_Neuron_EType.nrrd') -inh_nrrd.save_nrrd('./output/Generic_Inhibitory_Neuron_MType_Generic_Inhibitory_Neuron_EType.nrrd') diff --git a/exc_cell_splitting/mapping_cortex_all_to_exc_mtypes.csv b/exc_cell_splitting/mapping_cortex_all_to_exc_mtypes.csv deleted file mode 100644 index 9d2bc44..0000000 --- a/exc_cell_splitting/mapping_cortex_all_to_exc_mtypes.csv +++ /dev/null @@ -1,6 +0,0 @@ -layer,L2_IPC,L2_TPC:A,L2_TPC:B,L3_TPC:A,L3_TPC:B,L4_SSC,L4_TPC,L4_UPC,L5_TPC:A,L5_TPC:B,L5_TPC:C,L5_UPC,L6_BPC,L6_HPC,L6_IPC,L6_TPC:A,L6_TPC:C,L6_UPC -L2,0.082612842,0.129525291,0.787861866,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -L3,0,0,0,0.776524986,0.223475014,0,0,0,0,0,0,0,0,0,0,0,0,0 -L4,0,0,0,0,0,0.090735874,0.641289425,0.267974701,0,0,0,0,0,0,0,0,0,0 -L5,0,0,0,0,0,0,0,0,0.478764389,0.373704348,0.069744099,0.077787164,0,0,0,0,0,0 -L6,0,0,0,0,0,0,0,0,0,0,0,0,0.181041554,0.165265851,0.226502638,0.194968725,0.129358437,0.102862796