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load all_baseline before subsetting #11

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Jul 25, 2024
Merged

load all_baseline before subsetting #11

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923e472
load all_baseline before subsetting
chantelleleveille Jul 23, 2024
b42fd30
again load all_baseline before subsetting
chantelleleveille Jul 23, 2024
5ce985b
again load all_baseline before subsetting
chantelleleveille Jul 23, 2024
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3 changes: 2 additions & 1 deletion ...ph_analysis/analyses/dataset_images_for_figures/figure_dataset_formation_and_breakdown.py
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Expand Up @@ -23,7 +23,8 @@
colony = "medium"

# load the tracking CSV for medium from FMS
df = global_dataset_filtering.load_dataset_with_features(colony)
df = global_dataset_filtering.load_dataset_with_features()
df = df[df["colony"] == colony]
df_fmb = figure_helper.assemble_formation_middle_breakdown_dataframe(df)
# load the images for each timepoint
# %%
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3 changes: 2 additions & 1 deletion nuc_morph_analysis/analyses/dataset_images_for_figures/figure_dataset_processing_workflow.py
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Expand Up @@ -41,7 +41,8 @@
# show segmentations as sum projections of contours to emphasize 3D ness
use_cv_contours_for_3d = False

df = load_dataset_with_features(colony)
df = load_dataset_with_features()
df = df[df.colony == colony]
df["centroid_y_inv"] = 3120 - df["centroid_y"].values # seg.shape[1]-cy
df["centroid_z_inv"] = 109 - df["centroid_z"].values # seg.shape[0]-cz
df["centroid_z_inv_adjust"] = (
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3 changes: 2 additions & 1 deletion ...ph_analysis/analyses/dataset_images_for_figures/figure_dataset_save_3d_image_for_agave.py
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Expand Up @@ -35,7 +35,8 @@
# show segmentations as sum projections of contours to emphasize 3D ness
use_cv_contours_for_3d = False

df = load_dataset_with_features(name)
df = load_dataset_with_features()
df = df[df.colony == name]

# %%
# find the label number for the chosen track
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