Bone Analysis Workflow

The required input for the Dragonfly's Bone Analysis Wizard is high-resolution micro-CT image data of a bone specimen. Optional pre-processing steps can include re-orienting image data into the correct anatomical orientation, filtering to enhance data for the initial bone segmentation, and cropping to reduce data size and isolate the bone(s) of interest.

You can load 8, 16, and 32 bit image data saved in a number of file formats (TIFF, BMP, PNG, RAW, and ORSObject), as well as datasets saved in the DICOM file format.

Reorienting image data… In some cases, you may have to reorient your scan data so that the anatomical axes are correctly aligned for an analysis (see Reorienting Image Data).

Filtering… In some cases, you may need to filter your image data to reduce noise, detect edges, or apply another operation to facilitate initial bone segmentations (see Filtering Image Data).

Cropping… To reduce data sizes or in cases in which multiple bones are present, you can use the Crop tool as a pre-processing step (see Cropping Image Data).

Segment and Fill Bone… The first workflow step in the Bone Analysis Wizard is the task of segmenting the selected image and filling the initial segmentation (see Segmenting and Filling Bone). Inputs and settings for the first step are available on the Bone Segmentation and Filling page, as shown below.

Bone Segmentation and Filling page

You can refine initial bone segmentations and filled bone segmentations by removing unwanted objects, painting, applying ROI operations, and other tasks.

Separate Cortical/Trabecular Bone… The second step of the guided workflow, shown below, lets you choose a segmentation method ― Buie or Kohler ― for separating filled bone into cortical and trabecular components (see Separating Cortical and Trabecular Bone). These segmented regions, as well as the filled bone region of interest, can then be used as inputs for computing bone morphometric indices, as well as for computing scalar and vector fields and slice-by-slice measurements.

Filled Bone Separation page

You can refine automated segmentations by re-assigned mislabeled voxels, applying ROI operations, and other tasks.

Compute Global Measurements… Global measurements for common bone morphometric indices can be computed automatically from segmented bone, cortical, and trabecular areas, as well as from any region of interest that satisfies the requirements (see Computing Global Measurements). Results can be included in generated Bone Analysis reports or output in the comma-separated values (*.csv extension) file format.

Inputs, global measurements, and settings are available in the Global Measurements dialog, shown below.

Global Measurements dialog

Compute Scalar and Vector Fields… The inputs and settings to compute scalar values of volume thickness and vector fields of anisotropy are available as the next step in a bone analysis workflow on the Scalar and Vector Fields page (see Computing Scalar and Vector Fields).

Scalar and Vector Fields page

Compute slice-by-slice measurements… In addition to the global measurements available for bone morphometric indices, per slice measurements for image data and regions of interest are available in the Slice Analysis dialog. Slice analysis measurements are computed across all slices and results can be added to reports (see Computing Slice-by-Slice Measurements).

Generate report… The final step in most Bone Analysis workflows is to generate a report, which can include computed global measurements, distributions of bone mineral densities, plots of slice-by-slice measurements, and screen captures taken during the current session (see Generating Reports). Reports are saved in the PDF file format and are automatically formatted with a header that includes the project title, job ID, author(s), contact information, and creation date. You can also add your institution’s logo to your reports.