diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..68787a8177f51b86162e68d12991aa189d5e5983
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,163 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+
+outputs/
\ No newline at end of file
diff --git a/ProjectSegmentation3D_vec.py b/ProjectSegmentation3D_vec.py
index 78c1d3c9c5dd035b1836b85e09087d82c161ec83..885c97ada7203b8812bbe9aabb945d98aa77d532 100644
--- a/ProjectSegmentation3D_vec.py
+++ b/ProjectSegmentation3D_vec.py
@@ -2,7 +2,7 @@
 import numpy as np
 from DeepSlice.coord_post_processing.spacing_and_indexing import number_sections
 import json
-from VisuAlignLib_vec_original import triangulate,  forwardtransform_vec
+from VisuAlignWarpVec import triangulate,  forwardtransform_vec, transform_vec
 from glob import glob
 from tqdm import tqdm
 import cv2
@@ -67,7 +67,7 @@ def loadVisuAlignJson(filename):
     slices = vafile["slices"]
     return slices
 
-def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto'):
+def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto', nonLinear=True):
     Segmentation = cv2.imread(SegmentationPath)
 
     if pixelID == 'auto':
@@ -80,21 +80,41 @@ def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID='auto'):
     #transform pixels to registration space (the registered image and segmentation have different dimensions)
     SegHeight = Segmentation.shape[0]
     SegWidth  = Segmentation.shape[1]
-    points = applyTransformationToPoints(ID_pixels, slice, SegHeight, SegWidth)
-    # points = points.reshape(-1)
-    return points
-
-def applyTransformationToPoints(ID_pixels, slice,SegHeight, SegWidth):
     RegHeight = slice["height"]
     RegWidth  = slice["width"]
+    #this calculates reg/seg
     Yscale , Xscale = transformToRegistration(SegHeight,SegWidth,  RegHeight,RegWidth)
+    #this creates a triangulation using the reg width
     triangulation   = triangulate(RegWidth, RegHeight, slice["markers"])
+    #scale the seg coordinates to reg/seg
     scaledY,scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale)
-    newX, newY      = forwardtransform_vec(triangulation, scaledX, scaledY)
+    if nonLinear:
+        newX, newY = transform_vec(triangulation, scaledX, scaledY)
+    else:
+        newX, newY = scaledX, scaledY
+    #scale U by Uxyz/RegWidth and V by Vxyz/RegHeight
     points = transformToAtlasSpace(slice['anchoring'], newY, newX, RegHeight, RegWidth)
+    # points = points.reshape(-1)
     return points
 
-def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0]):
+# def applyTransformationToPoints(ID_pixels, slice,SegHeight, SegWidth, nonLinear=True):
+#     RegHeight = slice["height"]
+#     RegWidth  = slice["width"]
+#     #this calculates reg/seg
+#     Yscale , Xscale = transformToRegistration(SegHeight,SegWidth,  RegHeight,RegWidth)
+#     #this creates a triangulation using the reg width
+#     triangulation   = triangulate(RegWidth, RegHeight, slice["markers"])
+#     #scale the seg coordinates to reg/seg
+#     scaledY,scaledX = scalePositions(ID_pixels[0], ID_pixels[1], Yscale, Xscale)
+#     if nonLinear:
+#         newX, newY = transform_vec(triangulation, scaledX, scaledY)
+#     else:
+#         newX, newY = scaledX, scaledY
+#     #scale U by Uxyz/RegWidth and V by Vxyz/RegHeight
+#     points = transformToAtlasSpace(slice['anchoring'], newY, newX, RegHeight, RegWidth)
+#     return points
+
+def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0], nonLinear=True):
     slices = loadVisuAlignJson(QUINT_alignment)
     points = []
     segmentationFileTypes = [".png", ".tif", ".tiff", ".jpg", ".jpeg"] 
@@ -103,12 +123,12 @@ def FolderToAtlasSpace(folder, QUINT_alignment, pixelID=[0, 0, 0]):
     #order segmentations and sectionNumbers
     # Segmentations = [x for _,x in sorted(zip(SectionNumbers,Segmentations))]
     # SectionNumbers.sort()
-    for slice in tqdm(slices):
-        current_slice_number = int(slice["nr"])
-        SegmentationPath = Segmentations[SectionNumbers.index(current_slice_number)]
-        SegmentationPath =  SegmentationPath
-        # print(SegmentationPath)
-        points.extend(SegmentationToAtlasSpace(slice, SegmentationPath, pixelID))
+    for  SegmentationPath in Segmentations:
+        seg_nr = int(number_sections([SegmentationPath])[0])
+        current_slice_index = np.where([s["nr"]==seg_nr for s in slices])
+        current_slice = slices[current_slice_index[0][0]]
+        ##this converts the segmentation to a point cloud
+        points.extend(SegmentationToAtlasSpace(current_slice, SegmentationPath, pixelID, nonLinear))
     return points
 
 def WritePoints(pointsDict, filename, infoFile):
diff --git a/annotation_volumes/allen2022_colours.csv b/annotation_volumes/allen2022_colours.csv
new file mode 100644
index 0000000000000000000000000000000000000000..4d8bf976c32e526d63c3161bc5a1ed3954fad12e
--- /dev/null
+++ b/annotation_volumes/allen2022_colours.csv
@@ -0,0 +1,1328 @@
+id,r,g,b,1a,1b,1c,name,allenID
+1,97,23,22,1,1,1,TMv,1
+2,124,100,148,1,1,1,SSp-m6b,2
+3,45,110,140,1,1,1,sec,3
+4,87,181,14,1,1,1,IC,4
+5,11,248,9,1,1,1,int,6
+6,111,208,94,1,1,1,PSV,7
+7,9,47,174,1,1,1,grey,8
+8,162,233,124,1,1,1,SSp-tr6a,9
+9,55,139,65,1,1,1,SCig,10
+10,196,102,20,1,1,1,plf,11
+11,89,55,43,1,1,1,IF,12
+12,226,85,176,1,1,1,im,14
+13,23,10,250,1,1,1,PT,15
+14,237,48,27,1,1,1,6b,16
+15,197,147,134,1,1,1,SCiw,17
+16,64,107,196,1,1,1,nf,18
+17,159,28,70,1,1,1,IG,19
+18,61,70,91,1,1,1,ENTl2,20
+19,164,16,39,1,1,1,lotg,21
+20,135,229,117,1,1,1,PTLp,22
+21,158,58,212,1,1,1,AAA,23
+22,232,190,191,1,1,1,sif,25
+23,13,191,132,1,1,1,SCdg,26
+24,30,250,64,1,1,1,IGL,27
+25,37,198,60,1,1,1,ENTl6a,28
+26,65,80,126,1,1,1,sttl,29
+27,14,70,220,1,1,1,PVa,30
+28,234,26,106,1,1,1,ACA,31
+29,249,90,133,1,1,1,VISp6a,33
+30,149,96,29,1,1,1,icf,34
+31,191,86,92,1,1,1,III,35
+32,193,47,29,1,1,1,GU1,36
+33,239,115,75,1,1,1,lab,37
+34,36,221,231,1,1,1,PVH,38
+35,28,233,97,1,1,1,ACAd,39
+36,84,162,142,1,1,1,VISpm2/3,41
+37,2,53,79,1,1,1,SCdw,42
+38,187,8,16,1,1,1,apf,43
+39,77,214,145,1,1,1,ILA,44
+40,189,214,193,1,1,1,SPVOrdm,45
+41,79,233,75,1,1,1,mfbsma,46
+42,193,119,121,1,1,1,PVHam,47
+43,75,115,20,1,1,1,ACAv,48
+44,58,42,224,1,1,1,ipf,49
+45,127,0,110,1,1,1,PRC,50
+46,217,219,143,1,1,1,ILM,51
+47,94,85,58,1,1,1,ENTl3,52
+48,95,147,238,1,1,1,SPVOmdmd,53
+49,87,204,113,1,1,1,mfb,54
+50,118,196,53,1,1,1,PVHap,55
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+53,202,78,239,1,1,1,MT,58
+54,177,255,94,1,1,1,IMD,59
+55,251,248,121,1,1,1,ENTl6b,60
+56,83,129,1,1,1,1,SPVOmdmv,61
+57,235,49,142,1,1,1,mlf,62
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+59,61,50,114,1,1,1,AD,64
+60,199,170,212,1,1,1,pfs,65
+61,20,210,130,1,1,1,LT,66
+62,110,227,169,1,1,1,INC,67
+63,172,12,193,1,1,1,FRP1,68
+64,18,112,237,1,1,1,SPVOvl,69
+65,37,126,224,1,1,1,mfbsm,70
+66,182,59,39,1,1,1,PVHm,71
+67,53,5,82,1,1,1,ADP,72
+68,140,103,8,1,1,1,VS,73
+69,245,134,133,1,1,1,VISl6a,74
+70,101,25,79,1,1,1,DT,75
+71,64,234,248,1,1,1,INV,76
+72,171,232,169,1,1,1,SPVOcdm,77
+73,64,80,201,1,1,1,mcp,78
+74,35,81,88,1,1,1,PVHmm,79
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+77,67,30,15,1,1,1,NLLd,82
+78,200,6,1,1,1,1,IO,83
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+80,95,95,52,1,1,1,sct,85
+81,81,49,8,1,1,1,mtc,86
+82,164,184,231,1,1,1,PVHmpd,87
+83,81,29,249,1,1,1,AHN,88
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+85,168,7,215,1,1,1,NLLh,90
+86,101,110,163,1,1,1,IP,91
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+88,58,193,69,1,1,1,moV,93
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+1029,224,242,126,1,1,1,grv of CBX,1040
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+1055,50,79,126,1,1,1,VISam2/3,1066
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+1069,66,149,131,1,1,1,HIP,1080
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+1072,174,197,120,1,1,1,mfbse,1083
+1073,133,74,143,1,1,1,PRE,1084
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+1076,155,244,188,1,1,1,pce,1087
+1077,34,184,51,1,1,1,MGm,1088
+1078,45,75,140,1,1,1,HPF,1089
+1079,67,186,123,1,1,1,SSs5,1090
+1080,50,125,158,1,1,1,"CUL4, 5",1091
+1081,183,138,142,1,1,1,em,1092
+1082,60,118,116,1,1,1,PRNc,1093
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+1084,195,141,121,1,1,1,pcf,1095
+1085,203,194,181,1,1,1,AMd,1096
+1086,140,24,214,1,1,1,HY,1097
+1087,91,141,95,1,1,1,MDRNd,1098
+1088,210,223,44,1,1,1,fxs,1099
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+1099,226,64,236,1,1,1,SUMl,1110
+1100,16,26,245,1,1,1,SSp-tr5,1111
+1101,0,94,83,1,1,1,psf,1112
+1102,254,175,86,1,1,1,IAD,1113
+1103,210,3,43,1,1,1,VISal4,1114
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+1106,211,225,234,1,1,1,SUMm,1118
+1107,213,225,124,1,1,1,ppf,1119
+1108,17,50,50,1,1,1,IAM,1120
+1109,230,143,89,1,1,1,ENTl1,1121
+1110,210,133,175,1,1,1,icp,1123
+1111,1,195,12,1,1,1,PSCH,1124
+1112,134,43,141,1,1,1,ORBvl5,1125
+1113,193,204,133,1,1,1,TMd,1126
+1114,241,57,168,1,1,1,TEa2/3,1127
+1115,98,153,164,1,1,1,SSp-ll5,1128
+1116,148,238,70,1,1,1,IB,1129
+1117,234,28,153,1,1,1,iVIIn,1131
+1118,61,175,199,1,1,1,P-sen,1132
+1119,216,165,77,1,1,1,ENTmv5/6,1133
+1120,30,61,9,1,1,1,NLOT3,1139
+1121,237,185,117,1,1,1,TR1,1140
+1122,254,230,74,1,1,1,TR2,1141
+1123,33,96,167,1,1,1,TR3,1142
+1124,228,188,169,1,1,1,CBXgr,1143
+1125,211,88,67,1,1,1,CBXmo,1144
+1126,105,169,122,1,1,1,CBXpu,1145
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+1128,117,81,244,1,1,1,SIMgr,10672
+1129,251,19,191,1,1,1,SIMpu,10673
+1130,159,233,9,1,1,1,SIMmo,10674
+1131,184,91,27,1,1,1,ANcr1gr,10675
+1132,150,52,79,1,1,1,ANcr1pu,10676
+1133,94,9,188,1,1,1,ANcr1mo,10677
+1134,64,222,208,1,1,1,ANcr2gr,10678
+1135,34,71,24,1,1,1,ANcr2pu,10679
+1136,215,68,173,1,1,1,ANcr2mo,10680
+1137,199,163,248,1,1,1,PRMgr,10681
+1138,225,18,43,1,1,1,PRMpu,10682
+1139,81,219,30,1,1,1,PRMmo,10683
+1140,232,204,40,1,1,1,COPYgr,10684
+1141,44,203,152,1,1,1,COPYpu,10685
+1142,9,120,48,1,1,1,COPYmo,10686
+1143,19,141,28,1,1,1,PFLgr,10687
+1144,38,159,224,1,1,1,PFLpu,10688
+1145,107,63,153,1,1,1,PFLmo,10689
+1146,175,124,167,1,1,1,FLgr,10690
+1147,218,33,63,1,1,1,FLpu,10691
+1148,17,249,57,1,1,1,FLmo,10692
+1149,254,179,187,1,1,1,PAR1,10693
+1150,108,249,33,1,1,1,PAR2,10694
+1151,180,148,245,1,1,1,PAR3,10695
+1152,137,151,64,1,1,1,POST1,10696
+1153,25,104,172,1,1,1,POST2,10697
+1154,143,168,132,1,1,1,POST3,10698
+1155,95,149,16,1,1,1,PRE1,10699
+1156,225,21,203,1,1,1,PRE2,10700
+1157,162,215,93,1,1,1,PRE3,10701
+1158,187,152,122,1,1,1,DG-sgz,10702
+1159,140,210,52,1,1,1,DG-mo,10703
+1160,220,23,128,1,1,1,DG-po,10704
+1161,133,70,160,1,1,1,LINGgr,10705
+1162,228,48,9,1,1,1,LINGpu,10706
+1163,147,54,242,1,1,1,LINGmo,10707
+1164,48,95,59,1,1,1,CENT2gr,10708
+1165,202,129,36,1,1,1,CENT2pu,10709
+1166,16,77,65,1,1,1,CENT2mo,10710
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+1168,235,165,90,1,1,1,CENT3pu,10712
+1169,125,80,218,1,1,1,CENT3mo,10713
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+1171,209,62,113,1,1,1,CUL4pu,10715
+1172,94,20,232,1,1,1,CUL4mo,10716
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+1174,222,138,233,1,1,1,CUL5pu,10718
+1175,50,161,113,1,1,1,CUL5mo,10719
+1176,113,223,61,1,1,1,"CUL4, 5gr",10720
+1177,1,88,3,1,1,1,"CUL4, 5pu",10721
+1178,214,33,67,1,1,1,"CUL4, 5mo",10722
+1179,14,68,102,1,1,1,DECgr,10723
+1180,113,185,67,1,1,1,DECpu,10724
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+1182,43,104,15,1,1,1,FOTUgr,10726
+1183,252,189,254,1,1,1,FOTUpu,10727
+1184,248,218,240,1,1,1,FOTUmo,10728
+1185,82,6,47,1,1,1,PYRgr,10729
+1186,119,25,101,1,1,1,PYRpu,10730
+1187,94,165,46,1,1,1,PYRmo,10731
+1188,126,111,97,1,1,1,UVUgr,10732
+1189,211,38,74,1,1,1,UVUpu,10733
+1190,111,30,39,1,1,1,UVUmo,10734
+1191,188,237,227,1,1,1,NODgr,10735
+1192,221,45,54,1,1,1,NODpu,10736
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+1195,7,27,105,1,1,1,SS2/3,12994
+1196,44,28,41,1,1,1,SS4,12995
+1197,221,16,141,1,1,1,SS5,12996
+1198,6,182,57,1,1,1,SS6a,12997
+1199,156,213,87,1,1,1,SS6b,12998
+1200,100,33,26,1,1,1,SSp-un,182305689
+1201,246,156,164,1,1,1,SSp-un1,182305693
+1202,101,9,211,1,1,1,SSp-un2/3,182305697
+1203,7,106,118,1,1,1,SSp-un4,182305701
+1204,113,52,137,1,1,1,SSp-un5,182305705
+1205,72,113,173,1,1,1,SSp-un6a,182305709
+1206,167,244,92,1,1,1,SSp-un6b,182305713
+1207,104,5,46,1,1,1,retina,304325711
+1208,21,74,191,1,1,1,VISa,312782546
+1209,180,181,202,1,1,1,VISa1,312782550
+1210,123,233,151,1,1,1,VISa2/3,312782554
+1211,56,127,162,1,1,1,VISa4,312782558
+1212,193,62,67,1,1,1,VISa5,312782562
+1213,158,8,126,1,1,1,VISa6a,312782566
+1214,207,49,31,1,1,1,VISa6b,312782570
+1215,198,54,121,1,1,1,VISli,312782574
+1216,217,126,97,1,1,1,VISli1,312782578
+1217,162,141,96,1,1,1,VISli2/3,312782582
+1218,229,172,225,1,1,1,VISli4,312782586
+1219,180,57,11,1,1,1,VISli5,312782590
+1220,35,241,23,1,1,1,VISli6a,312782594
+1221,82,234,9,1,1,1,VISli6b,312782598
+1222,68,59,4,1,1,1,VISrl1,312782604
+1223,146,68,174,1,1,1,VISrl2/3,312782608
+1224,83,75,136,1,1,1,VISrl4,312782612
+1225,149,186,122,1,1,1,VISrl5,312782616
+1226,166,232,127,1,1,1,VISrl6a,312782620
+1227,131,50,39,1,1,1,VISrl6b,312782624
+1228,12,11,168,1,1,1,VISpor,312782628
+1229,53,98,188,1,1,1,VISpor1,312782632
+1230,21,221,221,1,1,1,VISpor2/3,312782636
+1231,95,59,211,1,1,1,VISpor4,312782640
+1232,7,220,187,1,1,1,VISpor5,312782644
+1233,22,168,44,1,1,1,VISpor6a,312782648
+1234,58,162,72,1,1,1,VISpor6b,312782652
+1235,36,206,205,1,1,1,VISrll,480149202
+1236,63,209,152,1,1,1,VISrll1,480149206
+1237,122,145,13,1,1,1,VISrll2/3,480149210
+1238,66,143,206,1,1,1,VISrll4,480149214
+1239,180,193,233,1,1,1,VISrll5,480149218
+1240,231,50,196,1,1,1,VISrll6a,480149222
+1241,226,216,234,1,1,1,VISrll6b,480149226
+1242,206,196,187,1,1,1,VISlla,480149230
+1243,31,93,221,1,1,1,VISlla1,480149234
+1244,191,209,156,1,1,1,VISlla2/3,480149238
+1245,1,55,70,1,1,1,VISlla4,480149242
+1246,37,32,81,1,1,1,VISlla5,480149246
+1247,77,234,201,1,1,1,VISlla6a,480149250
+1248,162,65,100,1,1,1,VISlla6b,480149254
+1249,170,17,30,1,1,1,VISmma,480149258
+1250,86,59,151,1,1,1,VISmma1,480149262
+1251,139,77,20,1,1,1,VISmma2/3,480149266
+1252,96,190,162,1,1,1,VISmma4,480149270
+1253,244,34,225,1,1,1,VISmma5,480149274
+1254,239,44,165,1,1,1,VISmma6a,480149278
+1255,146,104,187,1,1,1,VISmma6b,480149282
+1256,107,151,172,1,1,1,VISmmp,480149286
+1257,46,136,65,1,1,1,VISmmp1,480149290
+1258,42,1,184,1,1,1,VISmmp2/3,480149294
+1259,115,79,184,1,1,1,VISmmp4,480149298
+1260,242,69,229,1,1,1,VISmmp5,480149302
+1261,99,168,89,1,1,1,VISmmp6a,480149306
+1262,235,39,172,1,1,1,VISmmp6b,480149310
+1263,94,106,59,1,1,1,VISm,480149314
+1264,131,147,19,1,1,1,VISm1,480149318
+1265,144,29,124,1,1,1,VISm2/3,480149322
+1266,222,146,203,1,1,1,VISm4,480149326
+1267,84,189,49,1,1,1,VISm5,480149330
+1268,217,89,56,1,1,1,VISm6a,480149334
+1269,82,99,186,1,1,1,VISm6b,480149338
+1270,211,103,156,1,1,1,ProS,484682470
+1271,73,26,12,1,1,1,ProSd,484682475
+1272,214,73,73,1,1,1,ProSd-m,484682479
+1273,78,132,252,1,1,1,ProSd-sp,484682483
+1274,82,147,52,1,1,1,ProSd-sr,484682487
+1275,188,236,190,1,1,1,ProSv,484682492
+1276,2,205,195,1,1,1,ProSv-m,484682496
+1277,60,6,189,1,1,1,ProSv-sp,484682500
+1278,42,149,90,1,1,1,Prosv-sr,484682504
+1279,241,174,245,1,1,1,APr,484682508
+1280,25,224,182,1,1,1,scwm,484682512
+1281,7,135,129,1,1,1,ccb,484682516
+1282,82,171,168,1,1,1,or,484682520
+1283,145,156,130,1,1,1,ar,484682524
+1284,170,199,77,1,1,1,stc,484682528
+1285,162,223,228,1,1,1,LGd-sh,496345664
+1286,85,73,94,1,1,1,LGd-co,496345668
+1287,92,45,167,1,1,1,LGd-ip,496345672
+1288,77,201,103,1,1,1,FRP5,526157192
+1289,229,192,116,1,1,1,FRP6a,526157196
+1290,100,223,146,1,1,1,FRP6b,526322264
+1291,201,115,40,1,1,1,ORBm6b,527696977
+1292,220,208,119,1,1,1,LSS,549009199
+1293,158,154,226,1,1,1,RPF,549009203
+1294,71,130,122,1,1,1,InCo,549009207
+1295,205,150,224,1,1,1,MA3,549009211
+1296,203,98,18,1,1,1,P5,549009215
+1297,63,140,133,1,1,1,Acs5,549009219
+1298,144,136,52,1,1,1,PC5,549009223
+1299,83,190,194,1,1,1,I5,549009227
+1300,98,1,146,1,1,1,Eth,560581551
+1301,148,62,164,1,1,1,REth,560581555
+1302,24,91,121,1,1,1,Xi,560581559
+1303,189,171,43,1,1,1,PIL,560581563
+1304,116,210,168,1,1,1,PoT,563807435
+1305,64,176,54,1,1,1,IntG,563807439
+1306,188,14,190,1,1,1,VMPO,576073699
+1307,117,253,191,1,1,1,PeF,576073704
+1308,181,38,206,1,1,1,HATA,589508447
+1309,61,217,136,1,1,1,Pa5,589508451
+1310,149,235,252,1,1,1,VeCB,589508455
+1311,8,125,240,1,1,1,SCO,599626923
+1312,123,208,45,1,1,1,PDTg,599626927
+1313,119,78,176,1,1,1,MMl,606826647
+1314,78,10,28,1,1,1,MMm,606826651
+1315,92,236,23,1,1,1,MMp,606826655
+1316,249,73,179,1,1,1,MMd,606826659
+1317,247,145,28,1,1,1,Pa4,606826663
+1318,95,83,50,1,1,1,PN,607344830
+1319,37,180,73,1,1,1,IPR,607344834
+1320,59,118,147,1,1,1,IPC,607344838
+1321,106,74,141,1,1,1,IPA,607344842
+1322,119,83,96,1,1,1,IPL,607344846
+1323,119,95,65,1,1,1,IPI,607344850
+1324,7,73,191,1,1,1,IPDM,607344854
+1325,187,228,175,1,1,1,IPDL,607344858
+1326,224,228,204,1,1,1,IPRL,607344862
+1327,214,229,231,1,1,1,Su3,614454277
diff --git a/annotation_10.nrrd b/annotation_volumes/annotation_10.nrrd
similarity index 100%
rename from annotation_10.nrrd
rename to annotation_volumes/annotation_10.nrrd
diff --git a/itksnap_label_description.txt b/annotation_volumes/itksnap_label_description.txt
similarity index 100%
rename from itksnap_label_description.txt
rename to annotation_volumes/itksnap_label_description.txt
diff --git a/testMemoVec.py b/testMemoVec.py
index b9d11b780418a61c457657aa3b608ec8a3b8365e..51335cf3fb19925e885e4710197fdcbfef72b3b1 100644
--- a/testMemoVec.py
+++ b/testMemoVec.py
@@ -2,27 +2,13 @@ import time
 startTime = time.time()
 
 import numpy as np
-from VisuAlignLib_vec_original import triangulate,  forwardtransform_vec, forwardtransform
 import json
 from tqdm import tqdm
-import matplotlib.pyplot as plt
 import matplotlib
 matplotlib.use('TkAgg')
 
-from ProjectSegmentation3D_vec import FolderToAtlasSpace, getCentroidsAndArea, assignPointsToRegions
 
-import cv2
 
-# Segmentation = cv2.imread("ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s013_thumbnail_FinalSegmentation.png")
-#count the number of isolated segments
-# Segmentation[~np.all(Segmentation==255, axis=2)] = 0
-
-# centroids, area = getCentroidsAndArea(Segmentation, 4)
-
-    
-
-
-points = FolderToAtlasSpace("ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/", "PVMouse_81264_nonlin.json", pixelID=[255, 0, 0])
 
 #open colour txt file
 path = "itksnap_label_description.txt"
@@ -37,12 +23,23 @@ df.to_csv("allen2022_colours.csv", index=False)
 
 
 
-points = np.reshape(points, (-1, 3))
 
 # `read the annotation volume annotation_10.nrrd`
 import nrrd
 
 data, header = nrrd.read('annotation_10.nrrd')
+
+
+
+
+
+
+points = FolderToAtlasSpace("oneSection15/", "C68_nonlinear.json", pixelID=[255, 0, 255], nonLinear=True)
+
+
+points = np.reshape(points, (-1, 3))
+
+
 Points10um = points*2.5
 
 SwapData = np.transpose(data, (2,0,1))
@@ -53,6 +50,7 @@ regionDict = {region : [points[Regions==region]] for region in np.unique(Regions
 
 #show frequency of regions
 meshview = []
+points_all = []
 idx = 0
 for region in tqdm(regionDict):
     temp_points = np.array(regionDict[region])
@@ -62,17 +60,21 @@ for region in tqdm(regionDict):
         infoRow = pd.DataFrame([{"allenID": 0, "name": "background", "r": 255, "g": 255, "b": 255}])
     else:
         infoRow = df.loc[df['allenID'] == str(region)]
-    
-    meshview.append({
-        "idx": str(idx),
-        "count": str(len(temp_points)//3),
-        "name"  : str(infoRow["name"].values[0]),
-        "triplets": temp_points.tolist(),
-        "r": str(infoRow['r'].values[0]),
-        "g": str(infoRow['g'].values[0]),
-        "b": str(infoRow['b'].values[0])
-    })
-    idx += 1
+    points_all.extend(temp_points.tolist())
+    # meshview.append({
+    #     "idx": str(1),
+    #     "count": str(len(temp_points)//3),
+    #     # "name"  : str(infoRow["name"].values[0]),
+    #     "name":"1",
+    #     "triplets": temp_points.tolist(),
+    #     # "r": str(infoRow['r'].values[0]),
+    #     # "g": str(infoRow['g'].values[0]),
+    #     # "b": str(infoRow['b'].values[0])
+    #     "r": 0,
+    #     "g": 0,
+    #     "b": 255
+    # })
+    # idx += 1
     #write meshview json
 
 
@@ -81,5 +83,18 @@ for region in tqdm(regionDict):
     # print('Execution time in seconds: ' + str(executionTime))
     # points = points.reshape(-1)
     # write meshview json
-with open(f"colour_test.json", "w") as f:
+meshview.append({
+    "idx": str(1),
+    "count": str(len(temp_points)//3),
+    # "name"  : str(infoRow["name"].values[0]),
+    "name":"1",
+    "triplets": points_all,
+    # "r": str(infoRow['r'].values[0]),
+    # "g": str(infoRow['g'].values[0]),
+    # "b": str(infoRow['b'].values[0])
+    "r": 0,
+    "g": 0,
+    "b": 255
+})
+with open(f"colour_test_nonlin_notenpc.json", "w") as f:
     json.dump(meshview, f)
\ No newline at end of file
diff --git a/test_data/C68_nonlinear.json b/test_data/C68_nonlinear.json
new file mode 100644
index 0000000000000000000000000000000000000000..379b10773f1321fc2b2a2338f0e252cbf70dafcb
--- /dev/null
+++ b/test_data/C68_nonlinear.json
@@ -0,0 +1,51 @@
+{"name":"Test series","target":"ABA_Mouse_CCFv3_2017_25um.cutlas","target-resolution":[456.0, 528.0, 320.0],"slices":[
+{"filename":"1362_5366_7648_D1R_P49_F_C68_s001.png","nr":1,"width":13097,"height":18492,"anchoring":[230.14674200004373, 431.6345492635493, 253.5698870936448, -112.76432204654904, -0.4109929005257129, -7.325477280745247, 12.919121055200655, 43.01607526489645, -201.28316180093938],"markers":[[1924.7987220447287, 6521.669932177846, 1771.3727369542066, 7120.88319517709], [9516.726754005598, 6593.493318563987, 9107.92438764643, 7859.448379804069], [6651.210625258269, 704.0876162213747, 6583.369542066027, 668.8892238131123], [3865.8122205850673, 623.7552090750439, 3793.806176783812, 557.4076865109269], [10515.739094698367, 2164.1632917687984, 10460.862619808306, 2438.658628485305], [4266.506959663345, 16170.995796197203, 4616.727369542067, 15593.480030143179], [5915.030862690266, 5710.132885208391, 5662.813631522897, 6772.503391107763]]}, 
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\ No newline at end of file
diff --git a/PVMouse_81264_nonlin.json b/test_data/PVMouse_81264_nonlin.json
similarity index 100%
rename from PVMouse_81264_nonlin.json
rename to test_data/PVMouse_81264_nonlin.json
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s001_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s001_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s001_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s001_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s002_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s002_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s002_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s002_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s003_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s003_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s003_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s003_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s004_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s004_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s004_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s004_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s005_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s005_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s005_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s005_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s006_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s006_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s006_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s006_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s007_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s007_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s007_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s007_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s008_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s008_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s008_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s008_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s009_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s009_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s009_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s009_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s010_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s010_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s010_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s010_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s011_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s011_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s011_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s011_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s012_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s012_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s012_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s012_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s013_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s013_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s013_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s013_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s014_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s014_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s014_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s014_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s015_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s015_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s015_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s015_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s016_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s016_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s016_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s016_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s017_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s017_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s017_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s017_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s018_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s018_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s018_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s018_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s019_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s019_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s019_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s019_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s020_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s020_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s020_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s020_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s021_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s021_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s021_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s021_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s022_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s022_thumbnail_FinalSegmentation.png
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rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s022_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s022_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s023_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s023_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s023_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s023_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s024_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s024_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s024_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s024_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s025_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s025_thumbnail_FinalSegmentation.png
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rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s025_thumbnail_FinalSegmentation.png
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similarity index 100%
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similarity index 100%
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s028_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s029_thumbnail_FinalSegmentation.png
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similarity index 100%
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s030_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s031_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s031_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s031_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s032_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s032_thumbnail_FinalSegmentation.png
similarity index 100%
rename from ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s032_thumbnail_FinalSegmentation.png
rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s032_thumbnail_FinalSegmentation.png
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similarity index 100%
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s033_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s034_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s035_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s035_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s035_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s036_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s036_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s036_thumbnail_FinalSegmentation.png
diff --git a/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s037_thumbnail_FinalSegmentation.png b/test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s037_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s037_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s038_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s039_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s040_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s041_thumbnail_FinalSegmentation.png
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rename to test_data/ext-d000033_PVMouseExtraction_pub-Nutil_Quantifier_analysis-81264-Input_dir/ext-d000009_PVMouse_81264_Samp1_resize15__s042_thumbnail_FinalSegmentation.png
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