waveorder 2.2.0__py3-none-any.whl → 2.2.0rc0__py3-none-any.whl

waveorder/optics.py

@@ -133,7 +133,7 @@ def generate_pupil(frr, NA, lamb_in):
                     numerical aperture of the pupil function (normalized by the refractive index of the immersion media)
 
         lamb_in : float
-                    wavelength of the light in free space
+                    wavelength of the light (inside the immersion media)
                     in units of length (inverse of frr's units)
 
     Returns
@@ -225,103 +225,6 @@ def gen_sector_Pupil(fxx, fyy, NA, lamb_in, sector_angle, rotation_angle):
     return Pupil_sector
 
 
-def rotation_matrix(nu_z, nu_y, nu_x, wavelength):
-    nu_perp_squared = nu_x**2 + nu_y**2
-    nu_zz = wavelength * nu_z - 1
-
-    R_xx = (wavelength * nu_x**2 * nu_z + nu_y**2) / nu_perp_squared
-    R_yy = (wavelength * nu_y**2 * nu_z + nu_x**2) / nu_perp_squared
-    R_xy = nu_x * nu_y * nu_zz / nu_perp_squared
-
-    row0 = torch.stack((-wavelength * nu_y, -wavelength * nu_x), dim=0)
-    row1 = torch.stack((R_yy, R_xy), dim=0)
-    row2 = torch.stack((R_xy, R_xx), dim=0)
-
-    out = torch.stack((row0, row1, row2), dim=0)
-
-    # KLUDGE: fix the DC term manually, avoiding nan
-    out[..., 0, 0] = torch.tensor([[0, 0], [1, 0], [0, 1]])[..., None]
-
-    return torch.nan_to_num(out, nan=0.0)
-
-
-def generate_vector_source_defocus_pupil(
-    x_frequencies,
-    y_frequencies,
-    z_position_list,
-    defocus_pupil,
-    input_jones,
-    ill_pupil,
-    wavelength,
-):
-    ill_pupil_3d = torch.einsum(
-        "zyx,yx->zyx", torch.fft.fft(defocus_pupil, dim=0), ill_pupil
-    ).abs()  # make this real
-
-    freq_shape = z_position_list.shape + x_frequencies.shape
-
-    y_broadcast = torch.broadcast_to(y_frequencies[None, :, :], freq_shape)
-    x_broadcast = torch.broadcast_to(x_frequencies[None, :, :], freq_shape)
-    z_broadcast = np.sqrt(wavelength ** (-2) - x_broadcast**2 - y_broadcast**2)
-
-    # Calculate rotation matrix
-    rotations = rotation_matrix(
-        z_broadcast, y_broadcast, x_broadcast, wavelength
-    ).type(torch.complex64)
-
-    # TEMPORARY SIMPLIFY ROTATIONS "TURN OFF ROTATIONS"
-    # 3x2 IDENTITY MATRIX
-    rotations = torch.zeros_like(rotations)
-    rotations[1, 0, ...] = 1 
-    rotations[2, 1, ...] = 1
-
-    # Main calculation in the frequency domain
-    source_pupil = torch.einsum(
-        "ijzyx,j,zyx->izyx", rotations, input_jones, ill_pupil_3d
-    )
-
-    # Convert back to defocus pupil
-    source_defocus_pupil = torch.fft.ifft(source_pupil, dim=-3)
-
-    return source_defocus_pupil
-
-
-def generate_vector_detection_defocus_pupil(
-    x_frequencies,
-    y_frequencies,
-    z_position_list,
-    det_defocus_pupil,
-    det_pupil,
-    wavelength,
-):
-    # TODO: refactor redundancy with illumination pupil
-    det_pupil_3d = torch.einsum(
-        "zyx,yx->zyx", torch.fft.ifft(det_defocus_pupil, dim=0), det_pupil
-    )
-
-    # Calculate zyx_frequency grid (inelegant)
-    z_frequencies = torch.fft.ifft(z_position_list)
-    freq_shape = z_frequencies.shape + x_frequencies.shape
-    z_broadcast = torch.broadcast_to(z_frequencies[:, None, None], freq_shape)
-    y_broadcast = torch.broadcast_to(y_frequencies[None, :, :], freq_shape)
-    x_broadcast = torch.broadcast_to(x_frequencies[None, :, :], freq_shape)
-
-    # Calculate rotation matrix
-    rotations = rotation_matrix(
-        z_broadcast, y_broadcast, x_broadcast, wavelength
-    ).type(torch.complex64)
-
-    # Main calculation in the frequency domain
-    vector_detection_pupil = torch.einsum(
-        "jizyx,zyx->ijzyx", rotations, det_pupil_3d
-    )
-
-    # Convert back to defocus pupil
-    detection_defocus_pupil = torch.fft.fft(vector_detection_pupil, dim=-3)
-
-    return detection_defocus_pupil
-
-
 def Source_subsample(Source_cont, NAx_coord, NAy_coord, subsampled_NA=0.1):
     """
 
@@ -397,7 +300,7 @@ def generate_propagation_kernel(
         wavelength      : float
                         wavelength of the light in the immersion media
 
-        z_position_list : torch.tensor
+        z_position_list : torch.tensor or list
                         1D array of defocused z positions with the size of (Z)
 
     Returns
@@ -407,16 +310,15 @@ def generate_propagation_kernel(
 
     """
 
-    oblique_factor = ((1 - wavelength**2 * radial_frequencies**2)) ** (
-        1 / 2
-    ) / wavelength
-    oblique_factor = torch.nan_to_num(oblique_factor, nan=0.0)
+    oblique_factor = (
+        (1 - wavelength**2 * radial_frequencies**2) * pupil_support
+    ) ** (1 / 2) / wavelength
 
     propagation_kernel = pupil_support[None, :, :] * torch.exp(
         1j
         * 2
         * np.pi
-        * z_position_list[:, None, None]
+        * torch.tensor(z_position_list)[:, None, None]
         * oblique_factor[None, :, :]
     )
 
@@ -424,11 +326,7 @@ def generate_propagation_kernel(
 
 
 def generate_greens_function_z(
-    radial_frequencies,
-    pupil_support,
-    wavelength_illumination,
-    z_position_list,
-    axially_even=True,
+    radial_frequencies, pupil_support, wavelength_illumination, z_position_list
 ):
     """
 
@@ -445,14 +343,9 @@ def generate_greens_function_z(
         wavelength_illumination       : float
                         wavelength of the light in the immersion media
 
-        z_position_list : torch.tensor
+        z_position_list      : torch.tensor or list
                         1D array of defocused z position with the size of (Z,)
 
-        axially_even    : bool
-                        For backwards compatibility with legacy phase reconstruction.
-                        Ideally the legacy phase reconstruction should be unified with
-                        the new reconstructions, and this parameter should be removed.
-
     Returns
     -------
         greens_function_z       : torch.tensor
@@ -465,96 +358,46 @@ def generate_greens_function_z(
         * pupil_support
     ) ** (1 / 2) / wavelength_illumination
 
-    if axially_even:
-        z_positions = torch.abs(z_position_list[:, None, None])
-    else:
-        z_positions = z_position_list[:, None, None]
-
     greens_function_z = (
         -1j
         / 4
         / np.pi
         * pupil_support[None, :, :]
-        * torch.exp(1j * 2 * np.pi * z_positions * oblique_factor[None, :, :])
+        * torch.exp(
+            1j
+            * 2
+            * np.pi
+            * torch.tensor(z_position_list)[:, None, None]
+            * oblique_factor[None, :, :]
+        )
         / (oblique_factor[None, :, :] + 1e-15)
     )
 
     return greens_function_z
 
 
-def generate_defocus_greens_tensor(
-    fxx, fyy, G_fun_z, Pupil_support, lambda_in
-):
-    """
-
-    generate forward dyadic Green's function in u_x, u_y, z space
-
-    Parameters
-    ----------
-        fxx           : tensor.Tensor
-                        x component of 2D spatial frequency array with the size of (Ny, Nx)
-
-        fyy           : tensor.Tensor
-                        y component of 2D spatial frequency array with the size of (Ny, Nx)
-
-        G_fun_z       : tensor.Tensor
-                        forward Green's function in u_x, u_y, z space with size of (Nz, Ny, Nx)
-
-        Pupil_support : tensor.Tensor
-                        the array that defines the support of the pupil function with the size of (Ny, Nx)
-
-        lambda_in     : float
-                        wavelength of the light in the immersion media
-
-    Returns
-    -------
-        G_tensor_z    : tensor.Tensor
-                        forward dyadic Green's function in u_x, u_y, z space with the size of (3, 3, Nz, Ny, Nx)
-    """
-
-    fr = (fxx**2 + fyy**2) ** (1 / 2)
-    oblique_factor = ((1 - lambda_in**2 * fr**2) * Pupil_support) ** (
-        1 / 2
-    ) / lambda_in
-
-    diff_filter = torch.zeros((3,) + G_fun_z.shape, dtype=torch.complex64)
-    diff_filter[0] = (1j * 2 * np.pi * oblique_factor)[None, ...]
-    diff_filter[1] = (1j * 2 * np.pi * fyy * Pupil_support)[None, ...]
-    diff_filter[2] = (1j * 2 * np.pi * fxx * Pupil_support)[None, ...]
-
-    G_tensor_z = torch.zeros((3, 3) + G_fun_z.shape, dtype=torch.complex64)
-
-    for i in range(3):
-        for j in range(3):
-            G_tensor_z[i, j] = (
-                G_fun_z
-                * diff_filter[i]
-                * diff_filter[j]
-                / (2 * np.pi / lambda_in) ** 2
-            )
-            if i == j:
-                G_tensor_z[i, i] += G_fun_z
-
-    return G_tensor_z
-
-
 def gen_dyadic_Greens_tensor_z(fxx, fyy, G_fun_z, Pupil_support, lambda_in):
     """
-    keeping for backwards compatibility
 
     generate forward dyadic Green's function in u_x, u_y, z space
+
     Parameters
     ----------
         fxx           : numpy.ndarray
                         x component of 2D spatial frequency array with the size of (Ny, Nx)
+
         fyy           : numpy.ndarray
                         y component of 2D spatial frequency array with the size of (Ny, Nx)
+
         G_fun_z       : numpy.ndarray
                         forward Green's function in u_x, u_y, z space with size of (Ny, Nx, Nz)
+
         Pupil_support : numpy.ndarray
                         the array that defines the support of the pupil function with the size of (Ny, Nx)
+
         lambda_in     : float
                         wavelength of the light in the immersion media
+
     Returns
     -------
         G_tensor_z    : numpy.ndarray
@@ -584,6 +427,7 @@ def gen_dyadic_Greens_tensor_z(fxx, fyy, G_fun_z, Pupil_support, lambda_in):
             )
             if i == j:
                 G_tensor_z[i, i] += G_fun_z
+
     return G_tensor_z
 
 
@@ -717,60 +561,6 @@ def gen_dyadic_Greens_tensor(G_real, ps, psz, lambda_in, space="real"):
         )
 
 
-def generate_greens_tensor_spectrum(
-        zyx_shape, 
-        zyx_pixel_size,
-        wavelength,
-    ):
-    """
-    Parameters
-    ----------
-    zyx_shape : tuple
-    zyx_pixel_size : tuple
-    wavelength : float
-        wavelength in medium
-
-    Returns
-    -------
-    torch.tensor
-        Green's tensor spectrum 
-    """
-    Z, Y, X = zyx_shape
-    dZ, dY, dX = zyx_pixel_size
-
-    z_step = torch.fft.ifftshift(
-        (torch.arange(Z) - Z // 2) * dZ
-    )
-    y_step = torch.fft.ifftshift((torch.arange(Y) - Y // 2) * dY)
-    x_step = torch.fft.ifftshift((torch.arange(X) - X // 2) * dX)
-
-    zz = torch.broadcast_to(z_step[:, None, None], (Z, Y, X))
-    yy = torch.broadcast_to(y_step[None, :, None], (Z, Y, X))
-    xx = torch.broadcast_to(x_step[None, None, :], (Z, Y, X))
-
-    rr = torch.sqrt(xx**2 + yy**2 + zz**2)
-    rhat = torch.stack([zz, yy, xx], dim=0) / rr
-
-    scalar_g = torch.exp(1j * 2 * torch.pi * rr / wavelength) / (
-        4 * torch.pi * rr
-    )
-
-    eye = torch.zeros((3, 3, Z, Y, X))
-    eye[0, 0] = 1
-    eye[1, 1] = 1
-    eye[2, 2] = 1
-
-    Q = eye - torch.einsum("izyx,jzyx->ijzyx", rhat, rhat)
-    g_3d = Q * scalar_g
-    g_3d = torch.nan_to_num(g_3d)
-
-    G_3D = torch.fft.fftn(g_3d, dim=(-3, -2, -1))
-    G_3D = torch.imag(G_3D) * 1j
-    G_3D /= torch.amax(torch.abs(G_3D))
-
-    return G_3D
-    
-
 def compute_weak_object_transfer_function_2d(
     illumination_pupil, detection_pupil
 ):

waveorder/util.py

@@ -331,15 +331,12 @@ def gen_coordinate(img_dim, ps):
     return (xx, yy, fxx, fyy)
 
 
-def generate_frequencies(img_dim, ps):
+def generate_radial_frequencies(img_dim, ps):
     fy = torch.fft.fftfreq(img_dim[0], ps)
     fx = torch.fft.fftfreq(img_dim[1], ps)
-    fyy, fxx = torch.meshgrid(fy, fx, indexing="ij")
-    return fyy, fxx
 
+    fyy, fxx = torch.meshgrid(fy, fx, indexing="ij")
 
-def generate_radial_frequencies(img_dim, ps):
-    fyy, fxx = generate_frequencies(img_dim, ps)
     return torch.sqrt(fyy**2 + fxx**2)
 
 
@@ -2242,52 +2239,3 @@ def orientation_3D_continuity_map(
     retardance_pr_avg /= np.max(retardance_pr_avg)
 
     return retardance_pr_avg
-
-
-def pauli():
-    # yx order
-    # trace-orthogonal normalization
-    # torch.einsum("kij,lji->kl", pauli(), pauli()) == torch.eye(4)
-
-    # intensity, x-y, +45-(-45), LCP-RCP
-    # yx
-    # yx
-    a = 2**-0.5
-    sigma = torch.tensor(
-        [
-            [[a, 0], [0, a]],
-            [[-a, 0], [0, a]],
-            [[0, a], [a, 0]],
-            [[0, 1j * a], [-1j * a, 0]],
-        ]
-    )
-    return sigma
-
-
-def gellmann():
-    # zyx order
-    # trace-orthogonal normalization
-    # torch.einsum("kij,lji->kl", gellmann(), gellmann()) == torch.eye(9)
-    #
-    # lexicographical order of the Gell-Mann matrices
-    # 00, 1-1, 10, 11, 2-2, 2-1, 20, 21, 22
-    #
-    # zyx
-    # zyx
-    a = 3**-0.5
-    c = 2**-0.5
-    d = -(6**-0.5)
-    e = 2 * (6**-0.5)
-    return torch.tensor(
-        [
-            [[a, 0, 0], [0, a, 0], [0, 0, a]],
-            [[0, 0, -c], [0, 0, 0], [c, 0, 0]],
-            [[0, 0, 0], [0, 0, -c], [0, c, 0]],
-            [[0, -c, 0], [c, 0, 0], [0, 0, 0]],
-            [[0, 0, 0], [0, 0, c], [0, c, 0]],  #
-            [[0, c, 0], [c, 0, 0], [0, 0, 0]],
-            [[e, 0, 0], [0, d, 0], [0, 0, d]],
-            [[0, 0, c], [0, 0, 0], [c, 0, 0]],
-            [[0, 0, 0], [0, -c, 0], [0, 0, c]],  #
-        ], dtype=torch.complex64
-    )

waveorder/{visuals/jupyter_visuals.py → visual.py}

@@ -8,7 +8,11 @@ from ipywidgets import (
     Image,
     Layout,
     interact,
+    interactive,
+    fixed,
+    interact_manual,
     HBox,
+    VBox,
 )
 from matplotlib.colors import hsv_to_rgb
 from matplotlib.colors import Normalize
@@ -172,7 +176,7 @@ def image_stack_viewer_fast(
         else:
             raise ValueError('origin can only be either "upper" or "lower"')
 
-    im_wgt = Image(        
+    im_wgt = Image(
         value=im_dict[0],
         layout=Layout(height=str(size[0]) + "px", width=str(size[1]) + "px"),
     )
@@ -1924,4 +1928,4 @@ def orientation_3D_hist(
                 if colorbar:
                     fig.colorbar(img, ax=ax[row_idx, col_idx])
 
-    return fig, ax
+    return fig, ax

waveorder/waveorder_reconstructor.py

@@ -3,7 +3,6 @@ import matplotlib.pyplot as plt
 import itertools
 import time
 import os
-import warnings
 from numpy.fft import fft, ifft, fft2, ifft2, fftn, ifftn, fftshift, ifftshift
 from IPython import display
 from scipy.ndimage import uniform_filter
@@ -161,8 +160,8 @@ def instrument_matrix_calibration(I_cali_norm, I_meas):
 
 
 class waveorder_microscopy:
+
     """
-       DEPRECATED: Please see `waveorder.models` for maintained alternatives.
 
        waveorder_microscopy contains reconstruction algorithms for label-free
        microscopy with various types of dataset:
@@ -368,10 +367,6 @@ class waveorder_microscopy:
         initialize the system parameters for phase and orders microscopy
 
         """
-        warnings.warn(
-            "Please see `waveorder.models` for maintained alternatives.",
-            category=DeprecationWarning,
-        )
 
         t0 = time.time()
 
@@ -737,7 +732,9 @@ class waveorder_microscopy:
                 wave_vec_norm_x = self.lambda_illu * self.fxx
                 wave_vec_norm_y = self.lambda_illu * self.fyy
                 wave_vec_norm_z = (
-                    np.maximum(0, 1 - wave_vec_norm_x**2 - wave_vec_norm_y**2)
+                    np.maximum(
+                        0, 1 - wave_vec_norm_x**2 - wave_vec_norm_y**2
+                    )
                 ) ** (0.5)
 
                 incident_theta = np.arctan2(
@@ -4020,7 +4017,9 @@ class fluorescence_microscopy:
             S1_stack = cp.array(S1_stack)
             S2_stack = cp.array(S2_stack)
 
-            anisotropy = cp.asnumpy(0.5 * cp.sqrt(S1_stack**2 + S2_stack**2))
+            anisotropy = cp.asnumpy(
+                0.5 * cp.sqrt(S1_stack**2 + S2_stack**2)
+            )
             orientation = cp.asnumpy(
                 (0.5 * cp.arctan2(S2_stack, S1_stack)) % np.pi
             )

waveorder-2.2.0rc0.dist-info/METADATA

@@ -0,0 +1,147 @@
+Metadata-Version: 2.1
+Name: waveorder
+Version: 2.2.0rc0
+Summary: Wave-optical simulations and deconvolution of optical properties
+Author-email: CZ Biohub SF <compmicro@czbiohub.org>
+Maintainer-email: Talon Chandler <talon.chandler@czbiohub.org>, Shalin Mehta <shalin.mehta@czbiohub.org>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2019, Chan Zuckerberg Biohub
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/mehta-lab/waveorder
+Project-URL: Repository, https://github.com/mehta-lab/waveorder
+Project-URL: Issues, https://github.com/mehta-lab/waveorder/issues
+Keywords: simulation,optics,phase,scattering,polarization,label-free,permittivity,reconstruction-algorithm,qlipp,mipolscope,permittivity-tensor-imaging
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: MacOS
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy <2,>=1.21
+Requires-Dist: matplotlib >=3.1.1
+Requires-Dist: scipy >=1.3.0
+Requires-Dist: pywavelets >=1.1.1
+Requires-Dist: ipywidgets >=7.5.1
+Requires-Dist: torch >=2.2.1
+Provides-Extra: dev
+Requires-Dist: pytest ; extra == 'dev'
+Requires-Dist: pytest-cov ; extra == 'dev'
+
+# waveorder
+
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)
+[![Downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)
+[![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)
+[![Development Status](https://img.shields.io/pypi/status/napari.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
+
+This computational imaging library enables wave-optical simulation and reconstruction of optical properties that report microscopic architectural order.
+
+## Computational label-free imaging
+
+This vectorial wave simulator and reconstructor enabled the development of a new label-free imaging method, __permittivity tensor imaging (PTI)__, that measures density and  3D orientation of biomolecules with diffraction-limited resolution. These measurements are reconstructed from polarization-resolved images acquired with a sequence of oblique illuminations.
+
+The acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [preprint](https://doi.org/10.1101/2020.12.15.422951):
+
+```bibtex
+ L.-H. Yeh, I. E. Ivanov, B. B. Chhun, S.-M. Guo, E. Hashemi, J. R. Byrum, J. A. Pérez-Bermejo, H. Wang, Y. Yu, P. G. Kazansky, B. R. Conklin, M. H. Han, and S. B. Mehta, "uPTI: uniaxial permittivity tensor imaging of intrinsic density and anisotropy," bioRxiv 2020.12.15.422951 (2020).
+ ```
+
+In addition to PTI, `waveorder` enables simulations and reconstructions of subsets of label-free measurements with subsets of the acquired data:
+
+1. Reconstruction of 2D or 3D phase, projected retardance, and in-plane orientation from a polarization-diverse volumetric brightfield acquisition ([QLIPP](https://elifesciences.org/articles/55502))
+
+2. Reconstruction of 2D or 3D phase from a volumetric brightfield acquisition ([2D](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D (PODT)](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205) phase)
+
+3. Reconstruction of 2D or 3D phase from an illumination-diverse volumetric acquisition ([2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394&id=315599)/[3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940&id=349951) differential phase contrast)
+
+PTI provides volumetric reconstructions of mean permittivity ($\propto$ material density), differential permittivity ($\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:
+
+![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)
+
+
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D PODT, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP or PODT for label-free imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Correlative imaging
+
+In addition to label-free reconstruction algorithms, `waveorder` also implements widefield fluorescence and fluorescence polarization reconstruction algorithms for correlative label-free and fluorescence imaging.
+
+1. Correlative measurements of biomolecular density and orientation from polarization-diverse widefield imaging ([multimodal Instant PolScope](https://opg.optica.org/boe/fulltext.cfm?uri=boe-13-5-3102&id=472350))
+
+We provide an [example notebook](https://github.com/mehta-lab/waveorder/blob/main/examples/documentation/fluorescence_deconvolution/fluorescence_deconv.ipynb) for widefield fluorescence deconvolution.
+
+## Citation
+
+Please cite this repository, along with the relevant preprint or paper, if you use or adapt this code. The citation information can be found by clicking "Cite this repository" button in the About section in the right sidebar.
+
+## Installation
+
+(Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment:
+
+```sh
+conda create -y -n waveorder python=3.11
+conda activate waveorder
+```
+
+Install `waveorder` from PyPI:
+
+```sh
+pip install waveorder
+```
+
+Use `waveorder` in your scripts:
+
+```sh
+python
+>>> import waveorder
+```
+
+(Optional) Download the repository, install `jupyter`, and experiment with the example notebooks
+
+```sh
+git clone https://github.com/mehta-lab/waveorder.git
+pip install jupyter
+jupyter notebook ./waveorder/examples/
+```
+
+(M1 users) `pytorch` has [incomplete GPU support](https://github.com/pytorch/pytorch/issues/77764),
+so please use `export PYTORCH_ENABLE_MPS_FALLBACK=1`
+to allow some operators to fallback to CPU
+if you plan to use GPU acceleration for polarization reconstruction. 

waveorder-2.2.0rc0.dist-info/RECORD

@@ -0,0 +1,20 @@
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+waveorder/_version.py,sha256=y62tGqTh86kx1L4FG_Wu91vm4c-zkqBUqEkv0mTr0sY,414
+waveorder/background_estimator.py,sha256=gCIO6-232H0CGH4o6gnqW9KSYGOrXf5E9nD67WeF304,12399
+waveorder/correction.py,sha256=N0Ic6mqw3U7mqow4dKTOkNx2QYOLwedGNH7HiKV-M6s,3460
+waveorder/focus.py,sha256=4mg84Fe4V-oFplsuaU_VQU1_TEDoEfPggIAv6Is2dE4,6312
+waveorder/optics.py,sha256=-mHYRMzDUNAz8kwF8xAR8RFuAEkWZzczKv2wnU5NuVs,37640
+waveorder/stokes.py,sha256=Wk9ZimzICIZLh1CkB0kQSCSBLeugkDeydwXTPd-M-po,15186
+waveorder/util.py,sha256=3k810fpb7pIEcc4fii6gP4wTerxCtFYgG82SiDzUTtQ,69898
+waveorder/visual.py,sha256=SFzkQdMit3HyqTqrgzX4w5bRwz8QuwGumzVayi3DwDM,58171
+waveorder/waveorder_reconstructor.py,sha256=5-jlbK8gcJqHbFhiWt-TcETV5cdLHSAXq9O3JupPXD0,151942
+waveorder/waveorder_simulator.py,sha256=_HCmDZkACUGzgwnaI-q0PjsL1gRE55IQuaWw-wtAjCU,45856
+waveorder/models/inplane_oriented_thick_pol3d.py,sha256=Z7rfufrDeEkUYf2MlZsXyvKsZWHIJWujK357_z1BBg0,5809
+waveorder/models/isotropic_fluorescent_thick_3d.py,sha256=Pzi2kM1OGmwQIrI6b5h9OeIOGzHssG30Wv8zDi4n4PQ,5395
+waveorder/models/isotropic_thin_3d.py,sha256=E__ly_xF6Tw_bHLSHHPpd3p60t01LhIPiFrqfd5u1r4,8493
+waveorder/models/phase_thick_3d.py,sha256=itGav-JUDcs7YXxxtdtFK95CuaKR759o9ubL7ms8lBk,6590
+waveorder-2.2.0rc0.dist-info/LICENSE,sha256=auz4oGH1A-xZtoiR2zuXIk-Hii4v9aGgFVBqn7nfpms,1509
+waveorder-2.2.0rc0.dist-info/METADATA,sha256=KItkcQO-Bl3Gj-rutxx1V89YkVGYovr-QFo-OUPnAHI,8249
+waveorder-2.2.0rc0.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+waveorder-2.2.0rc0.dist-info/top_level.txt,sha256=i3zReXiiMTnyPk93W7aEz_oEfsLnfR_Kzl7PW7kUslA,10
+waveorder-2.2.0rc0.dist-info/RECORD,,

{waveorder-2.2.0.dist-info → waveorder-2.2.0rc0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any