diff --git a/PyNutil.py b/PyNutil.py
index 8d4510b9722f43dd8a2acb6505826bd5680ff4df..5daaf2d5d7a3bba662f5cdceaa217fb703c53d1b 100644
--- a/PyNutil.py
+++ b/PyNutil.py
@@ -130,4 +130,19 @@ def WritePoints(pointsDict, filename, infoFile):
     ]
     #write meshview json
     with open(filename, "w") as f:
-        json.dump(meshview, f)
\ No newline at end of file
+        json.dump(meshview, f)
+
+
+def labelPoints(points, label_volume, scale_factor=1):
+    #first convert the points to 3 columns
+    points = np.reshape(points, (-1,3))
+    #scale the points
+    points = points * scale_factor
+    #round the points to the nearest whole number
+    points = np.round(points).astype(int)
+    x = points[:,0]
+    y = points[:,1]
+    z = points[:,2]
+    #get the label value for each point
+    labels = label_volume[x,y,z]
+    return labels
diff --git a/annotation_volumes/annotation_10_reoriented.nrrd b/annotation_volumes/annotation_10_reoriented.nrrd
new file mode 100644
index 0000000000000000000000000000000000000000..9ea83344cd6d3fa962c1e6af77ed68d8608885dd
Binary files /dev/null and b/annotation_volumes/annotation_10_reoriented.nrrd differ
diff --git a/basic_workflow.py b/basic_workflow.py
index 933f64fe2846c934e419cfde7e0c0ae054a89044..be8db61d807cf0e3ea2a8a0a977e8dbb9feb8d86 100644
--- a/basic_workflow.py
+++ b/basic_workflow.py
@@ -3,18 +3,18 @@ import pandas as pd
 #nrrd just lets us open nrrd files
 import nrrd
 #import our function for converting a folder of segmentations to points
-from PyNutil import FolderToAtlasSpace
+from PyNutil import FolderToAtlasSpace, labelPoints
 
 
 
 #now we can use our function to convert the folder of segmentations to points
 points = FolderToAtlasSpace("test_data/oneSection15/", "test_data/C68_nonlinear.json", pixelID=[255, 0, 255], nonLinear=True)
-
 #first we need to find the label file for the volume
 label_path = "annotation_volumes//allen2022_colours.csv"
 #then the path to the volume
-volume_path = "annotation_volumes//annotation_10.nrrd"
+volume_path = "annotation_volumes//annotation_10_reoriented.nrrd"
 #read the label file
 label_df = pd.read_csv(label_path)
 #read the annotation volume, it also has a header but we don't need it
-data, header = nrrd.read(volume_path)
\ No newline at end of file
+data, header = nrrd.read(volume_path)
+#now we can get the labels for each point
diff --git a/reformat_allen_label.py b/scripts/reformat_allen_label.py
similarity index 100%
rename from reformat_allen_label.py
rename to scripts/reformat_allen_label.py
diff --git a/scripts/reorient_allen_volume.py b/scripts/reorient_allen_volume.py
new file mode 100644
index 0000000000000000000000000000000000000000..e5bbf128f8152b4b7df22fa78c58add4dbeb469e
--- /dev/null
+++ b/scripts/reorient_allen_volume.py
@@ -0,0 +1,14 @@
+"""
+This script was needed to reorient the Allen Volume to match the 
+orientation of meshview coordinates.
+"""
+
+import nrrd
+import numpy as np
+data, header = nrrd.read('../annotation_volumes/annotation_10.nrrd')
+# change the order of the axes
+data = np.transpose(data, (2,0,1))
+# flip two of the axes
+data = data[:, ::-1, ::-1]
+# write the new volume
+nrrd.write('../annotation_volumes/annotation_10_reoriented.nrrd', data, header=header)
diff --git a/testMemoVec.py b/testMemoVec.py
index 51335cf3fb19925e885e4710197fdcbfef72b3b1..21207e3f9c8bfb31157be1608f46a258b6d0fbab 100644
--- a/testMemoVec.py
+++ b/testMemoVec.py
@@ -2,11 +2,24 @@ import time
 startTime = time.time()
 
 import numpy as np
+from VisuAlignWarpVec 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)
+
+