DOI: 10.5281/zenodo.5951977
title: PTI datasets: 3D imaging

description: This dataset includes the following data reported in the PTI paper (link). These datasets can be read and processed using the provided notebooks (link) with the waveorder package (link). The zarr arrays (live one level below Col_x in the zarr files) in these datasets can also be visualized with the python image viewer (napari). You will need the ome-zarr plugin in napari and drag the zarr array to the napari viewer. 1. Anisotropic_target_small.zip includes two zarr files that save the raw intensity images and processed physical properties of the small anisotropic target (double line-scan, 300-fs pulse duration): - Anisotropic_target_small_raw.zarr: array size in the format of (PolChannel, IllumChannel, Z, Y, X) = (4, 9, 96, 300, 300) - Anisotropic_target_small_processed.zarr: (Pos0 - Stitched_f_tensor) array size in the format of (T, C, Z, Y, X) = (1, 9, 96, 300, 300) (Pos1 - Stitched_physical) array size in the format of (T, C, Z, Y, X) = (1, 5, 96, 300, 300) 2. Anisotropic_target_raw.zip includes the raw intensity images of another anisotropic target (single line-scan, 500-fs pulse duration): - data: 9 x 96 (pattern x z-slices) raw intensity images (TIFF) of the target with size of (2048, 2448) -&gt; 4 channels of (1024, 1224) - bg: - data: 9 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -&gt; 4 channels of (1024, 1224) - cali_images.pckl: pickle file that contains calibration curves of the polarization channels for this dataset 3. Anisotropic_target_processed.zip includes two zarr files that save the processed scattering potential tensor components and the processed physical properties of the anisotropic target (single line-scan, 500-fs pulse duration): - uPTI_stitched.zarr: (Stitched_f_tensor) array size in the format of (T, C, Z, Y, X) = (1, 9, 96, 1024, 1224) - uPTI_physical.zarr: (Stitched_physical) array size in the format of (T, C, Z, Y, X) = (1, 5, 96, 700, 700) (cropping the star target region) 4. Mouse_brain_aco_raw.zip includes the raw intensity images of the mouse brain section at aco region: - data: 9 x 96 (pattern x z-slices) raw intensity images (TIFF) of the mouse brain section with size of (2048, 2448) -&gt; 4 channels of (1024, 1224) - bg: - data: 9 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -&gt; 4 channels of (1024, 1224) - cali_images.pckl: pickle file that contains calibration curves of the polarization channels for this dataset 5. Mouse_brain_aco_processed.zip includes two zarr files that save the processed scattering potential tensor components and the processed physical properties of the mouse brain section at aco region: - uPTI_stitched.zarr: (Stitched_f_tensor) array size in the format of (T, C, Z, Y, X) = (1, 9, 96, 1024, 1224) - uPTI_physical.zarr: (Stitched_physical) array size in the format of (T, C, Z, Y, X) = (1, 5, 96, 1024, 1224) 6. Cardiomyocytes_(condition)_raw.zip includes two zarr files that save the raw PTI intensity images and the deconvolved fluorescence images of the cardiomyocytes with the specified (condition): - Cardiomyocytes_(condition)_raw.zarr: (Pos0) raw intensity images with the array size in the format of (PolChannel, IllumChannel, Z, Y, X) = (4, 9, 32, 1024, 1224) (Pos1) background intensity images with the array size in the format of (PolChannel, IllumChannel, Z, Y, X) = (4, 9, 1, 1024, 1224) - Cardiomyocytes_(condition)_fluor_decon.zarr: deconvolved fluorescence images with the array size in the format of (T, C, Z, Y, X) = (1, 3, 32, 1024, 1224) 7. Cardiomyocytes_(condition)_processed.zip includes two zarr files that save the processed scattering potential tensor components and the processed physical properties of the cardiomyocytes with the specified (condition): - uPTI_stitched.zarr: (Stitched_f_tensor) array size in the format of (T, C, Z, Y, X) = (1, 9, 32, 1024, 1224) - uPTI_physical.zarr: (Stitched_physical) array size in the format of (T, C, Z, Y, X) = (1, 5, 32, 1024, 1224) 8. cardiac_tissue_H_and_E_processed.zip and Human_uterus_section_H_and_E_raw.zip include the raw PTI intensity and H&E images of the cardiac tissue and human uterus section: - data: 10 x 40 (pattern x z-slices) raw intensity images (TIFF) of the target with size of (2048, 2448) -&gt; 4 channels of (1024, 1224), the last channel is for images acquired with LCD turned off (the light leakage needed to be subtracted from the data) - bg: - data: 10 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -&gt; 4 channels of (1024, 1224) - cali_images.pckl: pickle file that contains calibration curves of the polarization channels for this dataset - fluor: 3 x 40 (RGB x z-slices) raw H&E intensity images (TIFF) of the sample with size of (2048, 2448) - fluor_bg: 3 (RGB) raw H&E intensity images (TIFF) of the background with size of (2048, 2448) 9. cardiac_tissue_H_and_E_processed.zip and Human_uterus_section_H_and_E_processed.zip include three zarr files that save the processed scattering potential tensor components, the processed physical properties, and the white-balanced H&E intensities of the cardiac tissue and human uterus section: - uPTI_stitched.zarr: (Stitched_f_tensor) array size in the format of (T, C, Z, Y, X) = (1, 9, 40, 1024, 1224) - uPTI_physical.zarr: (Stitched_physical) array size in the format of (T, C, Z, Y, X) = (1, 5, 40, 1024, 1224) - H_and_E.zarr: (H_and_E) array size in the format of (T, C, Z, Y, X) = (1, 3, 40, 1024, 1224)
description: This work is supported by Chan Zuckerberg Biohub.