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 | Object_Label | 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_Condition | Metadata_Media | Metadata_Set | Metadata_Replicate | Metadata_Time | Metadata_FileName | Object_Label | 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 | 30C | S | 3 | 4 | 24 | 30C_2_3S_4 | 14 | 263.025755 | ... | 0.263252 | 0.538240 | 0.318621 | 220 | 0.662881 | 1629.588639 | 4183.333333 | S 30C | 2600.062893 | 2600.062893 |
| 1 | CBS1553 | 70 | 30C | S | 2 | 9 | 24 | 30C_2_2S_9 | 59 | 913.446401 | ... | 0.466440 | 0.690752 | 0.437718 | 172 | 2.239590 | 1357.262634 | 3020.666667 | S 30C | 2154.333333 | 2154.333333 |
| 2 | CBS1554 | 71 | 30C | S | 2 | 9 | 24 | 30C_2_2S_9 | 60 | 913.050952 | ... | 0.498056 | 0.740677 | 0.512969 | 173 | 3.302887 | 1357.262634 | 3020.666667 | S 30C | 2214.243243 | 2214.243243 |
3 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.