diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/report.tsv b/tests/test_data/nonlinear_allen_mouse/flat_files/report.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..ccba7b379e4f90b4c0912dbd5f0c2c2d32a5ff62
--- /dev/null
+++ b/tests/test_data/nonlinear_allen_mouse/flat_files/report.tsv
@@ -0,0 +1,6 @@
+snr	name	segmented	changed	stable%
+1	test_s001.png	64578	2991	95%
+2	test_s002.png	83702	34124	59%
+3	test_s003.png	93593	67152	28%
+4	test_s004.png	97022	44431	54%
+5	test_s005.png	92810	90411	2%
diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.flat
new file mode 100644
index 0000000000000000000000000000000000000000..e82b1e4b1019ffa83475844787dc639b2bbaa83f
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diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl.png
new file mode 100644
index 0000000000000000000000000000000000000000..b29e104e0c9760e86cddf9236e4ad4f0746d21dd
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diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s001_nl_rbw.png
new file mode 100644
index 0000000000000000000000000000000000000000..e370f2dfc395d6dbd4c5abc620288975190fe355
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diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.flat
new file mode 100644
index 0000000000000000000000000000000000000000..d4355f6e835a0b278c9e7e69b736e4214b7987e9
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diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s002_nl.png
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index 0000000000000000000000000000000000000000..8c4094b348097e921756405e7b1ee6d17da78ebd
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new file mode 100644
index 0000000000000000000000000000000000000000..e8f61cf8bbefbbaffe390a0ae8b8d004f7f53c89
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index 0000000000000000000000000000000000000000..632377cabe0d35595e116cf0c075d6aacbb393c7
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index 0000000000000000000000000000000000000000..a298dbf8a741cd0210c6b95c1e1eef768a1e15ce
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diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl.flat b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s004_nl.flat
new file mode 100644
index 0000000000000000000000000000000000000000..cc166d7bd1befd03c89b8fa9e857d56b979f9aba
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new file mode 100644
index 0000000000000000000000000000000000000000..150169f860a5ba7d17a4121fd6a8cb6c99bab27e
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diff --git a/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl_rbw.png b/tests/test_data/nonlinear_allen_mouse/flat_files/test_s005_nl_rbw.png
new file mode 100644
index 0000000000000000000000000000000000000000..ac3e9dadd08dfd6bd4649c22510da13075f1034d
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diff --git a/workflows/basic_example_custom_atlas.py b/workflows/basic_example_custom_atlas.py
index 5d9b9ed66792ecc58bc0ae3a5d8fcef1e570c731..3a281d4b8bcd5a075899ef6a873e6c51f7c53d95 100644
--- a/workflows/basic_example_custom_atlas.py
+++ b/workflows/basic_example_custom_atlas.py
@@ -12,6 +12,7 @@ from PyNutil import PyNutil
 ###The atlas_path is the path to the relevant atlas.nrrd
 ###The label_path is the path to the corresponding atlas .csv
 ###The object_cutoff is a cut-off for min object size
+### get_coordinates, if use_flat=True, place flat files in folder titled "flat_files" at same level as "segmentations" folder 
 
 pnt = PyNutil(
     segmentation_folder="../tests/test_data/linear_allen_mouse/",
@@ -20,6 +21,6 @@ pnt = PyNutil(
     atlas_path="../tests/test_data/allen_mouse_2017_atlas/annotation_25_reoriented_2017.nrrd",
     label_path="../tests/test_data/allen_mouse_2017_atlas//allen2017_colours.csv",
 )
-pnt.get_coordinates(object_cutoff=0)
+pnt.get_coordinates(object_cutoff=0, use_flat=True)
 pnt.quantify_coordinates()
 pnt.save_analysis("../test_result/test_linear_allen_mouse")