zenodoopen

PTI datasets: 3D imaging

This dataset includes the following data reported in the PTI paper (<a href="https://www.biorxiv.org/content/10.1101/2020.12.15.422951v2">link</a>). These datasets can be read and processed using the provided notebooks (<a href="https://github.com/mehta-lab/waveorder/tree/master/examples/uPTI_experiment">link</a>) with the waveorder package (<a href="https://github.com/mehta-lab/waveorder">link</a>). 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 (<a href="https://napari.org/">napari</a>). You will need the ome-zarr plugin in napari and drag the zarr array to the napari viewer.  1. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Anisotropic_target_small.zip?versionId=4e890f01-6442-41eb-bffa-0387cfae510b">Anisotropic_target_small.zip</a> 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:  <ul> <li>(Pos0 - Stitched_f_tensor) array size in the format of (T, C, Z, Y, X) = (1, 9, 96, 300, 300)</li> <li>(Pos1 - Stitched_physical) array size in the format of (T, C, Z, Y, X) = (1, 5, 96, 300, 300)</li> </ul>   2. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Anisotropic_target_raw.zip?versionId=d783651b-de1b-45fd-8e71-df17073ced40">Anisotropic_target_raw.zip</a> 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. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Anisotropic_target_processed.zip?versionId=4638a49f-82c2-4156-9c6c-e38742db0408">Anisotropic_target_processed.zip</a> 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. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Mouse_brain_aco_raw.zip?versionId=2c2a62bf-ab1a-4473-a064-4a58964aca56">Mouse_brain_aco_raw.zip</a> 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. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Mouse_brain_aco_processed.zip?versionId=22423258-3fe0-4240-b88e-e40f97321447">Mouse_brain_aco_processed.zip</a> 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: <ul> <li>(Pos0) raw intensity images with the array size in the format of (PolChannel, IllumChannel, Z, Y, X) = (4, 9, 32, 1024, 1224)</li> <li>(Pos1) background intensity images with the array size in the format of (PolChannel, IllumChannel, Z, Y, X) = (4, 9, 1, 1024, 1224)</li> </ul> - 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. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/cardiac_tissue_H_and_E_processed.zip?versionId=45a5c99c-b2fb-4a23-94f2-1ccc96e2d5a7">cardiac_tissue_H_and_E_processed.zip</a> and <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Human_uterus_section_H_and_E_raw.zip?versionId=83ded89e-b62a-4f06-be0f-f18d28eaf0aa">Human_uterus_section_H_and_E_raw.zip</a> 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. <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/cardiac_tissue_H_and_E_processed.zip?versionId=45a5c99c-b2fb-4a23-94f2-1ccc96e2d5a7">cardiac_tissue_H_and_E_processed.zip</a> and <a href="https://zenodo.org/api/files/c3b949a0-caf2-46ba-bb7c-b49192148ba9/Human_uterus_section_H_and_E_processed.zip?versionId=5080de3f-8527-40e6-bc80-6a6ec4f9bcf8">Human_uterus_section_H_and_E_processed.zip</a> 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)

ShareScore

40/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 16
Reuse readiness: 8
Engagement: 4

Topics

Label-free Microscopy Inverse algorithms Density Anisotropy 3D orientation Optic sign Myelination Organelle architecture Respiratory infection

PTI datasets: 3D imaging

Score breakdown

Topics

Your academic CV and NIH biosketch