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    Software

    Download our open-source codes

    EWALD

    EWALD is an open-source software that implements 3 optical diffraction tomography reconstruction algorithms, all based on Fourier Diffraction Theorem (FDT): (1) DI (Direct Inversion), GP (Gerchberg-Papoulis algorithm) and GPSC (Gerchberg-Papoulis with total-variation-based object-support constraint). It is dedicated for investigation of biological and technical samples, like cells, bacterias, optical fibers etc.

    GitHub

    ODT-SAS

    ODT-SAS is a new semi-automatic method that uses conventional approaches (not based on machine learning) to process optical diffraction tomography (ODT) images of biological cells. It enables 3D segmentation of whole biological cells and 2 types of their organelles: nucleolus and lipid structures.

    GitHub

    QPI-stitching-2D-3D

    QPI-stitching-2D-3D is a phase image preprocessing framework to be applied before stitching. It is compatible with the BigStitcher. It is intended to work with images acquired with our internally built hardware. Will require some minor tweaking to use with other naming conventions.

    GitHub

    Slicer for 3D RI engineering in two-photon polimerization

    Source code for the custom slicer that parses any 3D refractive index distribution (e.g. .mat file) into the .gwl file, suitable for 3D-printing via two-photon polymerization, such as Nanoscribe's PPGT2 system.

    Zenodo
    Datasets

    See our open-source datasets

    Numerical refractive index correction for the stitching procedure in tomographic quantitative phase imaging – dataset

    Raw volumetric data used in the work "Numerical refractive index correction for the stitching procedure in tomographic quantitative phase imaging" (doi.org/10.1364/BOE.466403)

    Zenodo

    Optical tomography measurements and reconstructions of a multiple-scattering 3d-printed microphantom

    This dataset contains 2 sets of measurements of a 3d-printed microphantom, carried out with optical diffraction tomography system at Warsaw University of Technology. The measurements are conducted for 2 different wavelengths: 633nm and 835nm.

    Zenodo

    Towards true volumetric refractive index investigation in tomographic phase microscopy at cellular level - dataset

    This dataset contains 6 files with reconstrucions of 3 different types of cells (SH-SY5Y neuroblastoma cells, A549 adenocarcinoma lung cells and HL-60 white blood cells), retrieved from optical diffraction tomography system measurements carried out at Warsaw University of Technology.

    Zenodo

    Influence of Yokukansan on refractive index of neuroblastoma cells - dataset

    This dataset contains 3 sets with files connected to holographic tomography (HT), fluorescence microscopy (FM) and Raman micro-spectroscopy (RmS) measurements. All measurements are from experiment on SH-SY5Y neuroblastoma cells with treatement of diferent doses of Yokukansan (YKS - Chinses herbal medicine herb).

    Zenodo

    Phase unwrapping using Deep Learning in Holographic Tomography - dataset.

    This dataset contains two types of data: phase images and trained model files.

    Zenodo

    Volumetric segmentation of biological cells and subcellular structures for optical diffraction tomography images - dataset

    This dataset includes 4 files with segmentation results for 4 different ODT reconstructions of SH-SY5Y neuroblastoma cell.

    Zenodo

    Segment and Support: a dual-purpose Deep Learning solution for Limited Angle Holographic Tomography - dataset

    This dataset constains training data of two types: Synthetic volumes:Containing randomly generated and placed spheres of various sizes. The dataset was augmented by adding noise, rotation, holes, flipping, blurring and shifting.

    Zenodo

    qtOCT: quantitative transmission optical coherence tomography - dataset

    This dataset includes 3 measurements captured with full-field swept-source OCT in transmission (t-FF-SS-OCT) that were used in the manuscript titled "qtOCT: quantitative transmission optical coherence tomography".

    Zenodo

    Achieving high quality 3D RI reconstructions from sparse data in high-throuput Holographic Tomography through CNN-based 2D projection synthesis - dataset

    This dataset constains training data of two types: Synthetic and technical volumes:This part of the dataset contains synthetically generated objects containing spherical or cube-like objects, augmented to include flipping, noise, shifting, stretching and shearing.

    Zenodo

    Tailored 3D microphantoms: an essesntial tool for quantitative phase tomography analysis of organoids - dataset

    Raw measurement data and processed results from three different ODT systems of the 3D-printed organoid phantoms

    Zenodo