(1) Background: Bone healing is a complex process that can not be replicated in its entirety in vitro. Research on bone healing still requires the animal model. The critical size femur defect (CSFD) in rats is a well-established model for fractures in humans that exceed the self-healing potential. New therapeutic approaches can be tested here in vivo. Histological, biomechanical, and radiological parameters are usually collected and interpreted. However, it is not yet clear to what extent they correlate with each other and how necessary it is to record all parameters. (2) Methods: The basis for this study was data from three animal model studies evaluating bone healing. The µCT and histological (Movat pentachrome, osteocalcin) datasets/images were reevaluated and correlation analyses were then performed. Two image processing procedures were compared in the analysis of the image data. (3) Results: There was a significant correlation between the histologically determined bone fraction (Movat pentachrome staining) and bending stiffness. Bone fraction determined by osteocalcin showed no prognostic value. (4) Conclusions: The evaluation of the image datasets using ImageJ is sufficient and simpler than the combination of both programs. Determination of the bone fraction using Movat pentachrome staining allows conclusions to be drawn about the biomechanics of the bone. A standardized procedure with the ImageJ software is recommended for determining the bone proportion.