diff --git a/PyNutil/main.py b/PyNutil/main.py
index 3255d35128a6aefcab83a0de76701553e6b3475c..50fe311efeb96a59babd9c66fb4f2b1097bbaf76 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -2,10 +2,10 @@ import json
 import os
 
 from .io.atlas_loader import load_atlas_data, load_custom_atlas
-from .data_analysis import quantify_labeled_points
+from .processing.data_analysis import quantify_labeled_points
 from .io.file_operations import save_analysis_output
-from .coordinate_extraction import folder_to_atlas_space
-from .counting_and_load import label_points
+from .processing.coordinate_extraction import folder_to_atlas_space
+from .processing.counting_and_load import label_points
 
 
 class PyNutil:
diff --git a/PyNutil/processing/__init__.py b/PyNutil/processing/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..b6e690fd59145ce8900fd9ab8d8a996ee7d33834
--- /dev/null
+++ b/PyNutil/processing/__init__.py
@@ -0,0 +1 @@
+from . import *
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/processing/coordinate_extraction.py
similarity index 99%
rename from PyNutil/coordinate_extraction.py
rename to PyNutil/processing/coordinate_extraction.py
index 9e1c3fd0c13e2b20751ffee7171c19a4c644da46..622d957bd1b03b771be3f6b5664053091c122c6a 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/processing/coordinate_extraction.py
@@ -1,6 +1,6 @@
 import numpy as np
 import pandas as pd
-from .io.read_and_write import load_visualign_json
+from ..io.read_and_write import load_visualign_json
 from .counting_and_load import flat_to_dataframe
 from .visualign_deformations import triangulate, transform_vec
 from glob import glob
@@ -8,7 +8,7 @@ import cv2
 from skimage import measure
 import threading
 import re
-from .io.reconstruct_dzi import reconstruct_dzi
+from ..io.reconstruct_dzi import reconstruct_dzi
 
 
 def number_sections(filenames, legacy=False):
diff --git a/PyNutil/counting_and_load.py b/PyNutil/processing/counting_and_load.py
similarity index 100%
rename from PyNutil/counting_and_load.py
rename to PyNutil/processing/counting_and_load.py
diff --git a/PyNutil/data_analysis.py b/PyNutil/processing/data_analysis.py
similarity index 100%
rename from PyNutil/data_analysis.py
rename to PyNutil/processing/data_analysis.py
diff --git a/PyNutil/generate_target_slice.py b/PyNutil/processing/generate_target_slice.py
similarity index 100%
rename from PyNutil/generate_target_slice.py
rename to PyNutil/processing/generate_target_slice.py
diff --git a/PyNutil/visualign_deformations.py b/PyNutil/processing/visualign_deformations.py
similarity index 100%
rename from PyNutil/visualign_deformations.py
rename to PyNutil/processing/visualign_deformations.py