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Commit a23fb790 authored by Sharon Yates's avatar Sharon Yates
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Update basic_example.py

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workflows/basic_example.py
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...@@ -10,7 +10,7 @@ from PyNutil import PyNutil ...@@ -10,7 +10,7 @@ from PyNutil import PyNutil
###The alignment json should be out of DeepSlice, QuickNII, or VisuAlign, it defines the sections position in an atlas ###The alignment json should be out of DeepSlice, QuickNII, or VisuAlign, it defines the sections position in an atlas
###The colour says which colour is the object you want to quantify in your segmentation. It is defined in RGB ###The colour says which colour is the object you want to quantify in your segmentation. It is defined in RGB
###Finally the atlas name is the relevant atlas from brainglobe_atlasapi you wish to use in Quantification. ###Finally the atlas name is the relevant atlas from brainglobe_atlasapi you wish to use in Quantification.
### get_coordinates, if use_flat=True, place flat files in folder titled "flat_files" at same level as "segmentations" folder .flat or .seg
pnt = PyNutil( pnt = PyNutil(
segmentation_folder="../tests/test_data/nonlinear_allen_mouse/", segmentation_folder="../tests/test_data/nonlinear_allen_mouse/",
...@@ -18,5 +18,5 @@ pnt = PyNutil( ...@@ -18,5 +18,5 @@ pnt = PyNutil(
colour=[0, 0, 0], colour=[0, 0, 0],
atlas_name="allen_mouse_25um", atlas_name="allen_mouse_25um",
) )
pnt.get_coordinates(object_cutoff=0) pnt.get_coordinates(object_cutoff=0, use_flat=True)
pnt.quantify_coordinates() pnt.quantify_coordinates()
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