diff --git a/scripts/PyNutil_test.json b/scripts/PyNutil_test.json
new file mode 100644
index 0000000000000000000000000000000000000000..f1e2bd453bafae1ad4f1a6b12c1b0f5936ae00b0
--- /dev/null
+++ b/scripts/PyNutil_test.json
@@ -0,0 +1,285 @@
+{
+ "name": "PyNutil_test.json",
+ "target": "ABA_Mouse_CCFv3_2017_25um.cutlas",
+ "target-resolution": [
+ 456,
+ 528,
+ 320
+ ],
+ "slices": [
+ {
+ "filename": "test_s001.png",
+ "width": 1500,
+ "height": 1000,
+ "snr": 1,
+ "format": "png",
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+ "filename": "test_s002.png",
+ "width": 1500,
+ "height": 1000,
+ "snr": 2,
+ "format": "png",
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+ "tilesize": 254,
+ "overlap": 1,
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\ No newline at end of file
diff --git a/test_data/PyNutil_test_2.waln b/scripts/PyNutil_test.waln
similarity index 100%
rename from test_data/PyNutil_test_2.waln
rename to scripts/PyNutil_test.waln
diff --git a/scripts/Tiling_script.py b/scripts/Tiling_script.py
new file mode 100644
index 0000000000000000000000000000000000000000..fd12fff1e4e3257a84937c5b5d7b2fb2740fcb40
--- /dev/null
+++ b/scripts/Tiling_script.py
@@ -0,0 +1,19 @@
+import os
+import sys
+import numpy as np
+import tifffile as tiff
+path_to_file = r"/home/harryc/Downloads/mouse-s23/ext-d000009_PVMouse_81265_Samp1__s023.tif"
+image_outdir = path_to_file.split(".")[0].split("/")[-1]
+if not os.path.exists(image_outdir):
+ os.makedirs(image_outdir)
+# Read the image
+img = tiff.imread(path_to_file)
+# Get the shape of the image
+shape = img.shape
+#Get the chunk size
+chunk_size = 512
+#crop the image and save each chunk
+for i in range(0, shape[0], chunk_size):
+ for j in range(0, shape[1], chunk_size):
+ chunk = img[i:i+chunk_size, j:j+chunk_size]
+ tiff.imsave("{}/chunk_{}_{}.tif".format(image_outdir,i, j), chunk)
\ No newline at end of file
diff --git a/scripts/waln_to_json.py b/scripts/waln_to_json.py
index f44cba5c843e35c862f967e15cf52faec996e4f5..342c30ff68084b75f25f363b156caf62bd071796 100644
--- a/scripts/waln_to_json.py
+++ b/scripts/waln_to_json.py
@@ -56,6 +56,6 @@ def waln_to_json(filename):
else:
pass
-waln_to_json("PyNutil_test_2.waln")
+waln_to_json("PyNutil_test.waln")
diff --git a/testOOP.py b/testOOP.py
index 3109bb82b350068bd4c4d1741a54cfe3ca82438e..63cb0854f0b12fb7ee3fe956b2ae78aa2a52168c 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -8,11 +8,11 @@ pnt = PyNutil(settings_file=r"PyNutil/test/test10_PyNutil_web.json")
##use_flat can be set to True if you want to use the flat file
## for method select between "all", "per_pixel" and "per_object"
-pnt.get_coordinates(object_cutoff=0, method="per_pixel", use_flat=False)
+pnt.get_coordinates(object_cutoff=0, method="all", use_flat=False)
pnt.quantify_coordinates()
-pnt.save_analysis("PyNutil/outputs/test10_PyNutil_web")
+pnt.save_analysis("PyNutil/outputs/test10_PyNutil_web_all")
# remove name, r, g, b, from pixel_
# add to region_areas df