How To: Correct Edge Effects in Plate Assays#

Colonies on the outer rows and columns of an agar plate often grow differently due to temperature gradients and humidity effects. Use EdgeCorrector to statistically identify and correct these biases.

[1]:

from phenotypic.data import load_meas
from phenotypic.analysis import EdgeCorrector

Load Measurement Data#

EdgeCorrector operates on measurement DataFrames, not on images directly. Start with a DataFrame containing colony measurements and grid position information.

[2]:

df = load_meas()
print(f"Shape: {df.shape}")
df.head()

Shape: (129, 245)

[2]:
Metadata_Condition Metadata_Media Metadata_Set Metadata_Replicate Metadata_Time Metadata_Strain Metadata_FileName ObjectLabel Bbox_CenterRR Bbox_CenterCC ... TextureGray_InfoCorrelation1-deg135-scale04 TextureGray_InfoCorrelation2-deg000-scale04 TextureGray_InfoCorrelation2-deg045-scale04 TextureGray_InfoCorrelation2-deg090-scale04 TextureGray_InfoCorrelation2-deg135-scale04 Metadata_StrainID TextureGray_HaralickVariance-avg-scale04 CorrectedCarryingCapacity_Intensity CorrectedCarryingCapacity_Area Metadata_Dataset
0 30C S 3 4 24 CBS11445 30C_2_3S_4 14 263.025755 327.103517 ... -0.033962 0.523065 0.263252 0.538240 0.318621 220 0.662881 1629.588639 4183.333333 S 30C
1 30C S 3 5 24 CBS11445 30C_2_3S_5 14 309.120466 291.332736 ... -0.035568 0.605276 0.243759 0.563349 0.376115 220 1.373371 1433.869174 3225.333333 S 30C
2 30C S 3 6 24 CBS11445 30C_2_3S_6 13 312.525658 262.907288 ... -0.068525 0.733840 0.519368 0.658842 0.497267 220 1.298390 1206.170181 2984.666667 S 30C
3 30C S 3 12 24 CBS11445 30C_2_3S_12 16 296.079598 305.151655 ... -0.057264 0.715456 0.470510 0.672158 0.475346 220 1.870195 1279.117711 3074.666667 S 30C
4 30C S 3 8 24 CBS11445 30C_2_3S_8 14 318.208931 260.158426 ... -0.034110 0.589887 0.358457 0.596423 0.342946 220 1.067527 1244.967859 2988.333333 S 30C

5 rows × 245 columns

Apply Edge Correction#

Specify the measurement column to correct (on), the grouping columns (groupby), and the grid dimensions.

[3]:

corrector = EdgeCorrector(
    on="Shape_Area",
    groupby=["Metadata_Strain"],
    nrows=8,
    ncols=12,
    top_n=3,
    pvalue=0.05,
)

[4]:

corrected = corrector.analyze(df)
corrected.head()

[4]:
Metadata_Strain Grid_RowMajorIdx Metadata_Time Metadata_Condition Metadata_Media Metadata_Set Metadata_Replicate Metadata_FileName ObjectLabel Bbox_CenterRR ... TextureGray_InfoCorrelation2-deg045-scale04 TextureGray_InfoCorrelation2-deg090-scale04 TextureGray_InfoCorrelation2-deg135-scale04 Metadata_StrainID TextureGray_HaralickVariance-avg-scale04 CorrectedCarryingCapacity_Intensity CorrectedCarryingCapacity_Area Metadata_Dataset EdgeCorrection_NewVal-Shape_Area EdgeCorrection_Cap-Shape_Area
0 CBS11445 13 24 30C S 3 4 30C_2_3S_4 14 263.025755 ... 0.263252 0.538240 0.318621 220 0.662881 1629.588639 4183.333333 S 30C 2123.000000 3018.454545
1 CBS11445 13 36 30C S 3 4 30C_3_3S_4 13 281.276198 ... 0.511469 0.752012 0.555040 220 3.543490 1629.588639 4183.333333 S 30C 2319.750000 3018.454545
2 CBS11445 13 48 30C S 3 2 30C_4_3S_2 15 251.863324 ... 0.407750 0.679685 0.401600 220 1.761140 1554.083914 4085.333333 S 30C 2526.866667 3018.454545
3 CBS11445 13 60 30C S 3 2 30C_5_3S_2 18 288.268624 ... 0.613829 0.796545 0.611889 220 1.791946 1554.083914 4085.333333 S 30C 3018.454545 3018.454545
4 CBS11445 13 72 30C S 3 8 30C_6_3S_8 11 226.486570 ... 0.491578 0.691649 0.521048 220 2.688246 1244.967859 2988.333333 S 30C 2773.194444 3018.454545

5 rows × 247 columns

The corrected DataFrame contains adjusted values for edge-affected colonies. The top_n parameter controls how many interior colonies are used as the reference baseline.