From a23fb79092521c1b347e92ff9dfac1d6ec28691b Mon Sep 17 00:00:00 2001 From: sharoncy Date: Thu, 7 Nov 2024 09:27:50 +0100 Subject: [PATCH] Update basic_example.py --- workflows/basic_example.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/basic_example.py b/workflows/basic_example.py index c1f7e9d..432a2cd 100644 --- a/workflows/basic_example.py +++ b/workflows/basic_example.py @@ -10,7 +10,7 @@ ###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 ###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( segmentation_folder="../tests/test_data/nonlinear_allen_mouse/", @@ -18,5 +18,5 @@ colour=[0, 0, 0], atlas_name="allen_mouse_25um", ) -pnt.get_coordinates(object_cutoff=0) +pnt.get_coordinates(object_cutoff=0, use_flat=True) pnt.quantify_coordinates()