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conorcamplissonconorcamplisson
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update file paths in 2D and 3D example notebooks
1 parent f0ff3a7 commit 6933490

4 files changed

Lines changed: 22 additions & 22 deletions

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‎notebooks/2D_fine_tune_training_demo.ipynb‎

Lines changed: 6 additions & 6 deletions
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@@ -26,10 +26,10 @@
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"source": [
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"from cellcyclenet import utils\n",
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"\n",
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"IMAGE_DIR = '../data/test_tiles/' # path to DAPI-stained FOVs\n",
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"MASK_DIR = '../data/test_masks/' # path to segmentation masks of FOVs \n",
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"LABEL_DIR = '../data/test_labels/' # path to label arrays of FOVs\n",
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"OUTPUT_DIR = '../data/test_SNI_label/' # path where labeled single-nucleus images will be saved\n",
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"IMAGE_DIR = '../example_data/2d/test_tiles/' # path to DAPI-stained FOVs\n",
30+
"MASK_DIR = '../example_data/2d/test_masks/' # path to segmentation masks of FOVs \n",
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"LABEL_DIR = '../example_data/2d/test_labels/' # path to label arrays of FOVs\n",
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"OUTPUT_DIR = '../example_data/2d/test_SNI_label/' # path where labeled single-nucleus images will be saved\n",
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"\n",
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"# generate labeled SNIs #\n",
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"'''\n",
@@ -107,7 +107,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "ccn_env",
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"language": "python",
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"name": "python3"
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},
@@ -121,7 +121,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.4"
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"version": "3.12.9"
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}
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},
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"nbformat": 4,

‎notebooks/2D_prediction_demo.ipynb‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -25,9 +25,9 @@
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"source": [
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"from cellcyclenet import utils\n",
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"\n",
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"IMAGE_DIR = '../data/test_tiles/' # path to DAPI-stained FOVs\n",
29-
"MASK_DIR = '../data/test_masks/' # path to segmentation masks of FOVs\n",
30-
"OUTPUT_DIR = '../data/test_SNI/' # path where single-nucleus images will be saved\n",
28+
"IMAGE_DIR = '../example_data/2d/test_tiles/' # path to DAPI-stained FOVs\n",
29+
"MASK_DIR = '../example_data/2d/test_masks/' # path to segmentation masks of FOVs\n",
30+
"OUTPUT_DIR = '../example_data/2d/test_SNI/' # path where single-nucleus images will be saved\n",
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"\n",
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"# generate unlabeled SNIs #\n",
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"'''\n",
@@ -74,7 +74,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "dask-cellpose",
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"display_name": "ccn_env",
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"language": "python",
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"name": "python3"
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},
@@ -88,7 +88,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.2"
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"version": "3.12.9"
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}
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},
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"nbformat": 4,

‎notebooks/3D_fine_tune_training_demo.ipynb‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -26,10 +26,10 @@
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"source": [
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"from cellcyclenet import utils\n",
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"\n",
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"IMAGE_DIR = '../data/test_tiles/' # path to DAPI-stained FOVs\n",
30-
"MASK_DIR = '../data/test_masks/' # path to segmentation masks of FOVs \n",
31-
"LABEL_DIR = '../data/test_labels/' # path to label arrays of FOVs\n",
32-
"OUTPUT_DIR = '../data/test_SNI_label/' # path where labeled single-nucleus images will be saved\n",
29+
"IMAGE_DIR = '../example_data/3d/test_tiles/' # path to DAPI-stained FOVs\n",
30+
"MASK_DIR = '../example_data/3d/test_masks/' # path to segmentation masks of FOVs \n",
31+
"LABEL_DIR = '../example_data/3d/test_labels/' # path to label arrays of FOVs\n",
32+
"OUTPUT_DIR = '../example_data/3d/test_SNI_label/' # path where labeled single-nucleus images will be saved\n",
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"\n",
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"# generate labeled SNIs #\n",
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"'''\n",
@@ -107,7 +107,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "ccn_env",
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"language": "python",
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"name": "python3"
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},
@@ -121,7 +121,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.4"
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"version": "3.12.9"
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}
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},
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"nbformat": 4,

‎notebooks/3D_prediction_demo.ipynb‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -25,9 +25,9 @@
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"source": [
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"from cellcyclenet import utils\n",
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"\n",
28-
"IMAGE_DIR = '../data/test_tiles/' # path to DAPI-stained FOVs\n",
29-
"MASK_DIR = '../data/test_masks/' # path to segmentation masks of FOVs\n",
30-
"OUTPUT_DIR = '../data/test_SNI/' # path where single-nucleus images will be saved\n",
28+
"IMAGE_DIR = '../example_data/3d/test_tiles/' # path to DAPI-stained FOVs\n",
29+
"MASK_DIR = '../example_data/3d/test_masks/' # path to segmentation masks of FOVs\n",
30+
"OUTPUT_DIR = '../example_data/3d/test_SNI/' # path where single-nucleus images will be saved\n",
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"\n",
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"# generate unlabeled SNIs #\n",
3333
"'''\n",
@@ -74,7 +74,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "dask-cellpose",
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"display_name": "ccn_env",
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"language": "python",
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"name": "python3"
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},
@@ -88,7 +88,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.2"
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"version": "3.12.9"
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}
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},
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"nbformat": 4,

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