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Quantitative 3D OPT and LSFM datasets of pancreata from mice with streptozotocin-induced diabetes


In this data descriptor, we present the datasets underlying this study, which are stored on the DRYAD data repository, dataset 1–37,8, and examples from each dataset to facilitate initial viewing and downloading, Sample dataset19.

Dataset 1: Volumetric and 3D-spatial OPT assessments of BCM distribution from pancreatic compartments (splenic lobe (SL), duodenal lobe (DL), gastric lobe (GL)) in a SHD and MLD diabetic mice, 1-, 2- and 3-weeks post injection in comparison to vehicle controls (SHDvCtrl, MLDvCtrl) and untreated controls (Ctrl) with corresponding blood glucose levels and body weights (Table S1)7.

Dataset 2: OPT analysis of BCM and GLUT2 3D expression intensities in pancreatic splenic lobes from SHD induced hyperglycaemia mice, in which glycemia was restored by islet transplantation (SHD + Tx). Pancreata were collected 28 days post administration of STZ and compared to vehicle control and SHD positive control with corresponding blood glucose levels and body weights (Table S2)8.

Dataset 3: High-resolution assessments of islet morphology using LSFM from representative samples from dataset 18.

Each dataset is subdivided into data records, based on the image processing pipeline (see Fig. 3). The provided raw projection views (data record A, datasets 1 & 2, data citation 1 & 5) were generated by an in house build near infrared -OPT scanner16 as *.tiff files. For data record B, tomographic 2D image datasets were processed and reconstructed into tomographic sections (datasets 1 & 2, data citation 2 and 6). Data record B further includes unprocessed LSFM generated sections (Dataset 3, data citation 9). For data record C, Z-sections from OPT and LSFM imaging were transformed into Imaris (*.ims) files for assessments of spatial and quantitative features of BCM distribution (dataset 1,2 & 3, data citation 3, 7 & 10). The resulting quantitative data were extracted from Imaris as Excel sheets (data record D, data citation 4 & 8) comprising numerical data on islets volumes, staining intensities, and islet sphericity, together with data on the pancreatic lobular anatomy. Jointly, the presented datasets may facilitate the planning, execution, and evaluation of a range of research undertakings pertaining to STZ-induced diabetes in rodents.

Fig. 3
figure 3

Data processing pipeline. Data record A from dataset 1 (Data record A, Data citation 1) and 2 (Data record A, Data citation 5) were processed using a set of in-house developed post-scanning computational scripts, DFTA (uniform alignment values) and CLAHE (equalizing the contrast of the insulin labelled islets) prior to reconstruction into tomographic images (image processing package “DSPOPT”, including DFTA (“A-value” tuning) and CLAHE can be found: https://github.com/ARDISDataset/DSPOPT). Data record B also include LSFM z-stacks from dataset 3 (Data citation 2, 6 and 9). The tomographic images converted to Imaris native.ims files were analysed (Data record C, 3, 7 and 10). Volumetric and spatial statistics was extracted in Imaris (Data record D, Data citation 4 and 8).

A schematic image of the organised data tree is displayed in Fig. 4. The data records describe the raw, processed (tomographic reconstructions), end point image datasets and quantitative/spatial data of the full BCM distribution in STZ-induced diabetic mice (SHD, MLD, SHD + Tx) and their healthy (C57BL/6) controls at 1-, 2- and 3-weeks post-administration, as well as vehicle controls (SHDvCtrl and MLDvCtrl). Note, the MLD group at the 1-week time point did not have any diabetic animals but were still included in the dataset.

Fig. 4
figure 4

Schematic illustration of data folder tree. Schematic illustration depicting the sub-organization of the datasets incorporated in the data descriptor including data records A-D, treatment groups, time points post STZ administration, sample IDs, imaging channels and scan location (LSFM).

Data record A

Raw projection datasets generated by OPT can be found in ‘Data record A Raw OPT projection views’ (Data record A Raw OPT projection views.zip, Data citation 1 and 5). Each individual scan is supported by a log file in *.txt format including scanning parameters such as exposure times or rotation steps. The individual image files are titled to indicate experimental group, age post-administration, animal ID, pancreatic lobe (splenic (SL), duodenal (DL) or gastric (GL)), channel (Insulin or Anatomy or for dataset 2 GLUT2) and step rotation number (1 step = 0.9 degrees of rotation) of projection image, e.g., ‘SHD_2wk_ID3_SL_Insulin_0398.tif‘.

Data record B

Data generated by tomographic reconstruction of OPT processed data (Axis of rotation, DFTA and CLAHE) can be found in ‘Data record B Tomographic images’ (Data record B Tomographic images.zip, Data citation 2 and 6), as well as raw generated LSFM z-sections as ‘Data record B LSFM z-stacks’ (Data record B LSFM z-stacks.zip, Data citation 9). The individual image sections of dataset 1 and 2 are annotated to indicate experimental group, age post-administration, animal ID, pancreatic lobe (SL, DL, GL respectively), channel (Insulin or Anatomy, or GLUT2 for dataset 2) and sequential z-stack number, e.g., ‘Ctrl_1wk_ID4_DL_Anatomy_0554.bmp’. Each LSFM section in record B in dataset 3 indicates experimental group, age post-administration, location of scanned volume (periphery or centre of the pancreatic splenic lobe), scan ID, channel (Insulin or Anatomy) and z-stack number, e.g., ‘MLD_STZ_2wk_SL_Center_2_Insulin_Z0003.ome.tif.

Data record C

Reconstructed data converted to *.ims format with 3D iso-surfaced volumes can be found in ‘Data record_C_Isosurfaced volume files’ (Data record_C_ Isosurfaced volume files.zip, Data citation 3 and 7) and for Dataset 3 Volume files (Data citation 10). The files contain (for datasets 1 and 2) iso-surfaces of islets of Langerhans based on the Insulin channel and of the lobular anatomy based on the anatomy channel, and 3D-volumes of the above-mentioned structures (dataset 3). They are annotated to indicate experimental group, age post-administration, animal ID and pancreatic lobe (splenic (SL), duodenal (DL) or gastric (GL)), e.g., ‘Ctrl_3w_ID4_SL.ims.

Data record D

Resulting quantitative data of processed 3D OPT volumes were retrieved from Imaris and can be found in ‘Data record D volumetric and spatial statistics’ (Data record D volumetric and spatial statistics.zip, Data citation 4 and 8). Reconstructed OPT scans produce isotropic voxels, which allows for reliable quantification, whereas LSFM scans in general have a distortion in the z-axis, as do the Ultramicroscope II used in this study due to the generation of the light sheet being two cones overlapping into each other rather than two parallel lines. Therefore, quantitative data is given for OPT data only. The OPT based Excel sheets are raw extracted numerical information. File titles indicate experimental group, age post-administration, animal ID, pancreatic lobe (splenic (SL), duodenal (DL) or gastric (GL)) and channel information, e.g., ‘Ctrl_3w_ID4_DL_anatomy.csv’. The csv files are subdivided into multiples files, each displaying a different parameter for the individual islets:

  • Volume

  • Area

  • Position

  • Sphericity

  • Intensity (centre, min, max, mean, median, sum)

  • Dimensional (x,y,z) diameter

  • Centre of homogenous mass

  • Distance to image border

  • Ellipsoid axis

  • Ellipticity (oblate/prolate)

  • Number of triangles

  • Number of vertices

  • Number of voxels

Supplementary Tables 3 and 4 display meta data of each sample to support data records and indicate each samples provenance and experimental manipulations performed as well as the resulting data outputs and which archived records they form.



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