Brightfield timelapse example

Install and import the dependencies

%pip uninstall basicpy -yq
%pip install basicpy -q

Note: you may need to restart the kernel to use updated packages.
Note: you may need to restart the kernel to use updated packages.

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

the value of the environment variable BASIC_DCT_BACKEND is not in ["JAX","SCIPY"]

Load the sample images

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

Downloading file 'timelapse_brightfield.npz' from 'https://github.com/peng-lab/BaSiCPy/raw/dev/data/timelapse_brightfield.npz' to '/home/docs/.cache/basicpy'.

<matplotlib.image.AxesImage at 0x7f9575418b80>

Fit the flatfield and darkfield

basic = BaSiC(get_darkfield=True, lambda_flatfield_coef=10)
basic.fit(images)

WARNING:absl:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
INFO:basicpy.basicpy:reweighting iteration 0
INFO:basicpy.basicpy:single-step optimization score: 6.403664087883953e-07.
INFO:basicpy.basicpy:mean of S: 1.0000001192092896.
INFO:basicpy.basicpy:Iteration 0 finished.
INFO:basicpy.basicpy:reweighting iteration 1
INFO:basicpy.basicpy:single-step optimization score: 9.878729088086402e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 1 finished.
INFO:basicpy.basicpy:reweighting score: 0.026257801800966263
INFO:basicpy.basicpy:elapsed time: 6.508570558000429 seconds
INFO:basicpy.basicpy:reweighting iteration 2
INFO:basicpy.basicpy:single-step optimization score: 9.937207323673647e-07.
INFO:basicpy.basicpy:mean of S: 1.0000001192092896.
INFO:basicpy.basicpy:Iteration 2 finished.
INFO:basicpy.basicpy:reweighting score: 0.026257801800966263
INFO:basicpy.basicpy:elapsed time: 8.188184904000082 seconds
INFO:basicpy.basicpy:reweighting iteration 3
INFO:basicpy.basicpy:single-step optimization score: 9.867982271316578e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 3 finished.
INFO:basicpy.basicpy:reweighting score: 0.17522761225700378
INFO:basicpy.basicpy:elapsed time: 9.789261509000426 seconds
INFO:basicpy.basicpy:reweighting iteration 4
INFO:basicpy.basicpy:single-step optimization score: 9.872994723991724e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 4 finished.
INFO:basicpy.basicpy:reweighting score: 0.006575890816748142
INFO:basicpy.basicpy:elapsed time: 11.465960357000768 seconds
INFO:basicpy.basicpy:Reweighting converged.
INFO:basicpy.basicpy:=== BaSiC fit finished in 11.551364736000323 seconds ===

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)

INFO:basicpy.basicpy:=== BaSiC transform started ===
INFO:basicpy.basicpy:unshading in 2 threads
INFO:basicpy.basicpy:=== BaSiC transform finished in 0.016013436000321235 seconds ===

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()