3D quantitative data sets in OPT and LSFM of the pancreas of mice with streptozotocin-induced diabetes mellitus.

In this data descriptor, we present the basic datasets for this study, which are stored in the DRYAD data warehouse, dataset 1-37,8and examples from each dataset to facilitate initial viewing and download, sample dataset19.

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

data set 2: OPT analysis of the intensity of BCM and GLUT2 3D expression in the pancreatic splenic lobes of hyperglycemic SHD mice, in which glycemia was restored by islet transplantation (SHD + Tx). Pancreata was collected 28 days after STZ administration and compared to vehicle control and SHD positive control with blood glucose levels and corresponding body weights (Table S2).8.

3 . data set: High-resolution assessments of islet morphology using LSFM from representative samples from the 1 . dataset8.

Each data set is divided into data records, based on the image processing pipeline (see Figure 3). The presented raw projection views (data log A, datasets 1 and 2, data citations 1 and 5) were generated by an internal device near the infrared scanner – OPT16 as files *. tiff. For data record B, 2D CT image data sets were processed and reconstructed in CT sections (data sets 1 and 2, data citations 2 and 6). Data record B further includes sections generated by unprocessed LSFM (data set 3, data citation 9). For data log C, Z sections from OPT and LSFM imaging were transformed into Imaris (*.ims) files to assess spatial and quantitative features of the BCM distribution (data set 1,2 and 3, data quotes 3, 7 and 10). The resulting quantitative data were extracted from Imaris in the form of Excel sheets (data log D, data citation 4 and 8) that include numerical data on islet sizes, staining intensity, and islet sphericity, as well as data on pancreatic lobule anatomy. Jointly, the presented data sets may facilitate the planning, implementation, and evaluation of a range of research tasks related to STZ-induced diabetes in rodents.

Figs. 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) was processed using a set of in-house developed post-scan computer scripts, DFTA (standardized alignment values) and CLAHE ( Insulin-labeled islet contrast equalization) prior to reconstruction in tomograms (the “DSPOPT” image processing package, including DFTA (“A-value adjustment”) and CLAHE can be found: https://github.com/ARDISDataset/DSPOPT). Data log B also includes LSFM z-stacks from data set 3 (data quote 2, 6 and 9). CT images converted to Imaris native.ims files (data log C, 3, 7 and 10) were analyzed. Volumetric and spatial statistics were extracted in Imaris (data log D, data citations 4 and 8).

A schematic image of the structured data tree is shown in Figure 4. Data records describe raw and processed endpoint image datasets (CT reconstruction) and quantitative/spatial data of the whole BCM distribution in STZ-induced diabetic mice (SHD, MLD, SHD + Tx ) and their healthy controls (C57BL/6) at 1, 2, and 3 weeks after administration, as well as the vehicle controls (SHDvCtrl and MLDvCtrl). Note that the MLD group at the 1-week time point had no animals with diabetes but was still included in the data set.

Figure 4
Figure 4

Schematic illustration of the data folder tree. Diagram showing the sub-organization of datasets embedded in the data descriptor including AD data records, treatment groups, time points after STZ administration, sample identifiers, imaging channels, and survey site (LSFM).

data record a

Raw OPT projection datasets can be found in “A Raw OPT data log projection views” (A Raw OPT data log projection views.zip, Data citation 1 and 5). Each individual scan is supported by a log file in *.txt format including scan parameters such as exposure times or rotation steps. Individual image files are labeled to indicate experimental group, age after administration, animal ID, pancreatic lobe (spleen (SL), duodenum (DL) or stomach (GL)), duct (insulin, anatomy or for data set 2 GLUT2) and The step rotation number (one step = 0.9° rotation) of the projection image, for example, “SHD_2wk_ID3_SL_Insulin_0398.tif”.

record data with

The data from the tomographic reconstruction of the OPT processed data (rotation axis, DFTA and CLAHE) can be found in ‘Data log B tomography images’ (data log B tomography images .zip, data citation 2 and 6), And also the raw output partitions z LSFM as “data log B LSFM z-stacks” (data log B LSFM z-stacks.zip, data citation 9). Individual image sections for data set 1 and 2 were annotated to indicate the experimental group, age after administration, animal ID, pancreatic lobe (SL, DL, GL respectively), duct (insulin or anatomy, or GLUT2 for data set 2) and sequenced z-number The heap, for example, “Ctrl_1wk_ID4_DL_Anatomy_0554.bmp”. Each LSFM section in log B in data set 3 indicates experimental group, age after administration, location of scanned volume (periphery or center of pancreatic splenic lobe), scan ID and duct (insulin or anatomy) and z-stack number, eg ‘MLD_STZ_2wk_SL_Center_2_Insulin_Z0003.ome’ .tif.

data record c

Reconstructed data converted to *.ims format with 3D isometric 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 citation 3 and 7) bulk files (Data Citation 10) . The files (for datasets 1 and 2) contain equal surfaces of the islets of Langerhans based on the insulin duct and lobular anatomy based on the canal dissection and 3D volumes of the above structures (data set 3). Annotated to indicate the experimental group, age after administration, animal ID, and lobe of the pancreas (spleen (SL), duodenum (DL) or stomach (GL)), eg, ‘Ctrl_3w_ID4_SL.ims.

data record d

Quantitative data generated from processed 3D OPT volumes were retrieved from Imaris and can be found in “Data log D Volumetric and spatial statistics” (data log D Volumetric and spatial statistics. zip, data citations 4 and 8). Reconstructed OPT scans produce homogeneous pixels, allowing reliable quantification, whereas LSFM scans generally have z-axis distortion, as is the case with the Ultramicroscope II used in this study due to the generation of the photonic sheet that are overlapping two cones in Both of them instead of two parallel lines. Therefore, quantitative data are presented for OPT data only. OPT-based Excel sheets are extracted raw numeric information. File titles indicate experimental group, age after administration, animal ID, pancreatic lobe (spleen (SL), duodenum (DL) or stomach (GL)), and duct information, eg, “Ctrl_3w_ID4_DL_anatomy.csv”. csv files are divided into multiple files, each of which displays a different parameter for the individual islands:

  • amount

  • region

  • Site

  • spherical

  • Intensity (center, minimum, maximum, average, average, total)

  • Dimensions (x, y, z) diameter

  • homogeneous center of mass

  • The distance to the border of the image

  • elliptical axis

  • elliptic (oblate / inflated)

  • number of triangles

  • number of heads

  • voxel number

Supplementary Tables 3 and 4 present the metadata for each sample to support the data records and indicate each source of the samples and experimental treatments performed as well as the resulting data outputs and the archived records that constitute them.

#quantitative #data #sets #OPT #LSFM #pancreas #mice #streptozotocininduced #diabetes #mellitus

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