Package: waveorder
waveorderThis computational imaging library enables wave-optical simulation and reconstruction of optical properties that report microscopic architectural order.Computational label-free imagingThis 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 followingpreprint: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,waveorderenables simulations and reconstructions of subsets of label-free measurements with subsets of the acquired data:Reconstruction of 2D or 3D phase, projected retardance, and in-plane orientation from a polarization-diverse volumetric brightfield acquisition (QLIPP)Reconstruction of 2D or 3D phase from a volumetric brightfield acquisition (2D/3D (PODT)phase)Reconstruction of 2D or 3D phase from an illumination-diverse volumetric acquisition (2D/3Ddifferential 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:Theexample notebooksillustrate 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 ournapari plugin,recOrder-napari.Correlative imagingIn addition to label-free reconstruction algorithms,waveorderalso implements widefield fluorescence and fluorescence polarization reconstruction algorithms for correlative label-free and fluorescence imaging.Correlative measurements of biomolecular density and orientation from polarization-diverse widefield imaging (multimodal Instant PolScope)We provide anexample notebookfor widefield fluorescence deconvolution.CitationPlease 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) installanacondaand create a virtual environment:condacreate-y-nwaveorderpython=3.9
condaactivatewaveorderInstallwaveorderfrom PyPI:pipinstallwaveorderUsewaveorderin your scripts:python
>>>importwaveorder(Optional) Download the repository, installjupyter, and experiment with the example notebooksgitclonehttps://github.com/mehta-lab/waveorder.git
pipinstalljupyter
jupyternotebook./waveorder/examples/(Optional) Use NVIDIA GPUs by installingcupywiththese instructions. Check thatcupyis properly installed withpython
>>>importcupyTo use GPUs inwaveordersetuse_gpu=Truewhen initializing the simulator and reconstructor classes.