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PTI datasets: 3D imaging

PTI datasets: 3D imaging
PTI datasets: 3D imaging
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) -> 4 channels of (1024, 1224) - bg: - data: 9 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -> 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) -> 4 channels of (1024, 1224) - bg: - data: 9 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -> 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) -> 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) -> 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)
Zenodo
Byrum, Janie
5dbe0fc2-4f1e-4bfa-9d49-91999bd8a0b7
Ivanov, Ivan
c9f3e74c-9421-4d39-828f-3a6bdc26ec4d
Wang, Huijun
71d8cb32-58db-496b-8e5d-cf378dda5a53
Yeh, Li-Hao
dddf215a-fb71-4a74-bb1c-06ac8a21666e
Kazansky, Peter
a5d123ec-8ea8-408c-8963-4a6d921fd76c
Conklin, Bruce
612d69b5-f839-48ab-9869-241b1c70400c
Guo, Syuan-Ming
bf38d3b7-460d-4023-8be6-942188859587
Pérez-Bermejo, Juan
c19f765e-0c1e-4856-b2d4-02342be331b5
Yu, Yanhao
a46f1df6-fa8f-475c-b1aa-b98205266f6c
Hashemi, Ezzat
9cb58a70-1365-4fdb-9e6b-7a0707e1b15a
Mehta, Shalin
7abf7cd7-be65-47e2-bc7b-7d079fb767ac
Foltz, Cameron
a20e685b-b523-446a-80f0-5e9438be5da4
Han, May
4e7ce2b4-ff25-40ba-ae9a-da0eabd96206
Chhun, Bryant
d8f0eebf-d2a9-428e-bebb-fe2212b7d1bf
Byrum, Janie
5dbe0fc2-4f1e-4bfa-9d49-91999bd8a0b7
Ivanov, Ivan
c9f3e74c-9421-4d39-828f-3a6bdc26ec4d
Wang, Huijun
71d8cb32-58db-496b-8e5d-cf378dda5a53
Yeh, Li-Hao
dddf215a-fb71-4a74-bb1c-06ac8a21666e
Kazansky, Peter
a5d123ec-8ea8-408c-8963-4a6d921fd76c
Conklin, Bruce
612d69b5-f839-48ab-9869-241b1c70400c
Guo, Syuan-Ming
bf38d3b7-460d-4023-8be6-942188859587
Pérez-Bermejo, Juan
c19f765e-0c1e-4856-b2d4-02342be331b5
Yu, Yanhao
a46f1df6-fa8f-475c-b1aa-b98205266f6c
Hashemi, Ezzat
9cb58a70-1365-4fdb-9e6b-7a0707e1b15a
Mehta, Shalin
7abf7cd7-be65-47e2-bc7b-7d079fb767ac
Foltz, Cameron
a20e685b-b523-446a-80f0-5e9438be5da4
Han, May
4e7ce2b4-ff25-40ba-ae9a-da0eabd96206
Chhun, Bryant
d8f0eebf-d2a9-428e-bebb-fe2212b7d1bf

(2022) PTI datasets: 3D imaging. Zenodo doi:10.5281/zenodo.5951978 [Dataset]

Record type: Dataset

Abstract

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) -> 4 channels of (1024, 1224) - bg: - data: 9 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -> 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) -> 4 channels of (1024, 1224) - bg: - data: 9 (pattern) raw intensity images (TIFF) of the background with size of (2048, 2448) -> 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) -> 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) -> 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)

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Published date: 2 February 2022

Identifiers

Local EPrints ID: 474426
URI: http://eprints.soton.ac.uk/id/eprint/474426
PURE UUID: f99b1f92-5196-4de3-b904-2a135425f71a

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Date deposited: 22 Feb 2023 17:33
Last modified: 01 Aug 2023 17:17

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Contributors

Contributor: Janie Byrum
Contributor: Ivan Ivanov
Contributor: Huijun Wang
Contributor: Li-Hao Yeh
Contributor: Peter Kazansky
Contributor: Bruce Conklin
Contributor: Syuan-Ming Guo
Contributor: Juan Pérez-Bermejo
Contributor: Yanhao Yu
Contributor: Ezzat Hashemi
Contributor: Shalin Mehta
Contributor: Cameron Foltz
Contributor: May Han
Contributor: Bryant Chhun

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