Channel alignment and shift correction

Check fluorescence registration before interpreting profiles or object positions. BactoScoop exposes several related operations with different effects.

Object alignment

batch_detect_objects(..., align=True) uses the object detection alignment path for the requested channel. The five-channel notebook enables this for the outer-membrane channel C2 and leaves it disabled for C3–C5. This is an example-specific choice.

Shifted geometry

batch_shift_correction constructs shifted contours, midlines, and meshes. use_shifted_contours=True selects stored shifted geometry in feature calculation. It requires the relevant shifted data to exist; enabling the flag does not itself perform shift correction.

Signal cropping

shift_signal=True activates signal handling during supported measurements. The profiling and membrane implementations use their respective cropping and optional-shift utilities. The objects method receives extra positional arguments through *args and does not use shift_signal as a general object-coordinate transformation.

Inspect these operations separately because a successful field match does not prove subpixel registration, and changing one flag does not automatically change every measurement. See the C2 alignment figure in Five-channel walkthrough: membranes and multichannel profiles and the exact API signatures in Parameter reference.

import bactoscoop.plot as bplt
fig = bplt.plot_C2_alignment(
    ic.image_objects[0], cell_id=43, channel="C2",
    channel_label="Outer membrane", show_objects=True,
)

Choose a cell ID present in your own retained image before calling a cell-level plot. The number above comes from the supplied five-channel walkthrough.