Brain whole slide image 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.wsi_brain()
plt.imshow(images[12])

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

<matplotlib.image.AxesImage at 0x7f6e690a1b80>

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: 5.862551688551321e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 0 finished.
INFO:basicpy.basicpy:reweighting iteration 1
INFO:basicpy.basicpy:single-step optimization score: 8.586401349930384e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 1 finished.
INFO:basicpy.basicpy:reweighting score: 0.4913370609283447
INFO:basicpy.basicpy:elapsed time: 4.790914952000094 seconds
INFO:basicpy.basicpy:reweighting iteration 2
INFO:basicpy.basicpy:single-step optimization score: 9.414103487870307e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 2 finished.
INFO:basicpy.basicpy:reweighting score: 0.03791121393442154
INFO:basicpy.basicpy:elapsed time: 5.414380725000228 seconds
INFO:basicpy.basicpy:reweighting iteration 3
INFO:basicpy.basicpy:single-step optimization score: 6.040669404683285e-07.
INFO:basicpy.basicpy:mean of S: 0.9999999403953552.
INFO:basicpy.basicpy:Iteration 3 finished.
INFO:basicpy.basicpy:reweighting score: 0.2741871774196625
INFO:basicpy.basicpy:elapsed time: 6.003654062999885 seconds
INFO:basicpy.basicpy:reweighting iteration 4
INFO:basicpy.basicpy:single-step optimization score: 6.231510951693053e-07.
INFO:basicpy.basicpy:mean of S: 1.0000001192092896.
INFO:basicpy.basicpy:Iteration 4 finished.
INFO:basicpy.basicpy:reweighting score: 0.023092152550816536
INFO:basicpy.basicpy:elapsed time: 6.616932478000308 seconds
INFO:basicpy.basicpy:reweighting iteration 5
INFO:basicpy.basicpy:single-step optimization score: 6.461627890530508e-07.
INFO:basicpy.basicpy:mean of S: 0.9999999403953552.
INFO:basicpy.basicpy:Iteration 5 finished.
INFO:basicpy.basicpy:reweighting score: 0.014786623418331146
INFO:basicpy.basicpy:elapsed time: 7.216995929000404 seconds
INFO:basicpy.basicpy:reweighting iteration 6
INFO:basicpy.basicpy:single-step optimization score: 6.661320526291092e-07.
INFO:basicpy.basicpy:mean of S: 1.0.
INFO:basicpy.basicpy:Iteration 6 finished.
INFO:basicpy.basicpy:reweighting score: 0.056590840220451355
INFO:basicpy.basicpy:elapsed time: 7.836563122999905 seconds
INFO:basicpy.basicpy:reweighting iteration 7
INFO:basicpy.basicpy:single-step optimization score: 7.044488938845461e-07.
INFO:basicpy.basicpy:mean of S: 1.0000001192092896.
INFO:basicpy.basicpy:Iteration 7 finished.
INFO:basicpy.basicpy:reweighting score: 0.0066207703202962875
INFO:basicpy.basicpy:elapsed time: 8.434077275000163 seconds
INFO:basicpy.basicpy:Reweighting converged.
INFO:basicpy.basicpy:=== BaSiC fit finished in 8.51443919400026 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 0.05921558000045479 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()