Brightfield timelapse example

Install and import the dependencies

# install the basicpy in case of Google Colaboratory
try:
    import google.colab

    %pip uninstall -yq basicpy
    %pip install --upgrade -q basicpy
except ModuleNotFoundError:
    pass

from basicpy import BaSiC
from basicpy import datasets as bdata
from matplotlib import pyplot as plt

Load the sample images

images = bdata.timelapse_brightfield()
plt.imshow(images[10])

Downloading file 'timelapse_brightfield.npz' from 'doi:10.5281/zenodo.6974039/timelapse_brightfield.npz' to '/home/docs/.cache/basicpy'.

<matplotlib.image.AxesImage at 0x7fd4716acf10>

Fit the flatfield and darkfield

basic = BaSiC(get_darkfield=True, smoothness_flatfield=1)
basic.fit(images)

Plot the fit results

fig, axes = plt.subplots(1, 3, figsize=(9, 3))
im = axes[0].imshow(basic.flatfield)
fig.colorbar(im, ax=axes[0])
axes[0].set_title("Flatfield")
im = axes[1].imshow(basic.darkfield)
fig.colorbar(im, ax=axes[1])
axes[1].set_title("Darkfield")
axes[2].plot(basic.baseline)
axes[2].set_xlabel("Frame")
axes[2].set_ylabel("Baseline")
fig.tight_layout()

Correct the original images

images_transformed = basic.transform(
    images,
)

Plot the corrected results

i = 12
fig, axes = plt.subplots(1, 2, figsize=(6, 3))
im = axes[0].imshow(images[i])
fig.colorbar(im, ax=axes[0])
axes[0].set_title("Original")
im = axes[1].imshow(images_transformed[i])
fig.colorbar(im, ax=axes[1])
axes[1].set_title("Corrected")
fig.tight_layout()