Pycroscopy3D

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Pycroscopy3D is a collection of tools for microscopy.

Features

• Easy 3D-stack manipulation with multipagetiff
• Straightforward extraction of average PSF from a volumetric image of point-like objects
• 3D deconvolution (using iocbio/deconvolve
• Stack registration (using ANTsPy)

Example use

import pycroscopy3D as pycro

# load a stack (volumetric image) of fluorescent beads
stack_path = "./psf_stack.tiff"
s = pycro.read_stack(stack_path)
s

Multi-Page Stack of 2500 pages. (dx=dy=1, dz=1, crop=[0, 470, 0, 317]], page limits=[0, 2500])

# plot the Z-max-projection of the stack
pycro.plot_flatten(s)

# initialize the average PSF calculation
psf = pycro.PSF(s,size_tolerance=0.7)
psf

PSF generator: found 33 objects, 17 rejected (wrong size).

# Calculate the average PSG
psf.calc_mean_psf()

Find centroids: 100%|██████████| 16/16 [00:57<00:00,  3.62s/it]
Crop PSFs: 100%|██████████| 16/16 [00:00<00:00, 12555.45it/s]

# plot the mean PSF
mean_psf = psf.mean_PSF
pycro.orthogonal_views(mean_psf)