PTI datasets: 3D imaging

DOI10.5281/zenodo.5951978Zenodo5951978MaRDI QIDQ6696526

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 2 February 2022

Copyright license: No records found.

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 (liveone 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.zipincludes 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.zipincludes the raw intensity imagesof anotheranisotropic 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) - 4 channels of (1024, 1224) - bg:- data: 9 (pattern) raw intensity images (TIFF) of the backgroundwith size of (2048, 2448) - 4 channels of (1024, 1224) - cali_images.pckl: pickle filethat contains calibration curves of the polarization channels for this dataset 3.Anisotropic_target_processed.zipincludes two zarr files that save the processed scattering potential tensor componentsand 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.zipincludes the raw intensity imagesof the mouse brain section at aco region: - data: 9 x 96(pattern x z-slices) raw intensity images (TIFF) of the mouse brain sectionwith size of (2048, 2448) - 4 channels of (1024, 1224) - bg:- data: 9 (pattern) raw intensity images (TIFF) of the backgroundwith size of (2048, 2448) - 4 channels of (1024, 1224) - cali_images.pckl: pickle filethat contains calibration curves of the polarization channels for this dataset 5.Mouse_brain_aco_processed.zipincludes two zarr files that save the processed scattering potential tensor componentsand 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.zipincludes two zarr files that save the raw PTI intensity images and the deconvolved fluorescence images of the cardiomyocyteswith 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.zipincludes two zarr files that save the processed scattering potential tensor componentsand the processed physical properties of the cardiomyocyteswith 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.zipandHuman_uterus_section_H_and_E_raw.zipincludethe raw PTI intensity and HE imagesof the cardiac tissue and human uterus section: - data: 10x 40 (pattern x z-slices) raw intensity images (TIFF) of the target with size of (2048, 2448) - 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 backgroundwith size of (2048, 2448) - 4 channels of (1024, 1224) - cali_images.pckl: pickle filethat contains calibration curves of the polarization channels for this dataset - fluor: 3x 40 (RGB x z-slices) raw HE intensity images (TIFF) of the samplewith size of (2048, 2448) - fluor_bg: 3 (RGB) raw HE intensity images (TIFF) of the backgroundwith size of (2048, 2448) 9.cardiac_tissue_H_and_E_processed.zipandHuman_uterus_section_H_and_E_processed.zipincludethree zarr files that save the processed scattering potential tensor components, the processed physical properties, and the white-balanced HE 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)

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