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Bone histomorphometry allows quantitative evaluation of bone micro-architecture, bone formation, and bone remodeling by providing an insight to cellular changes. Histomorphometry plays an important role in monitoring changes in bone properties because of systemic skeletal diseases like osteoporosis and osteomalacia. Besides, quantitative evaluation plays an important role in fracture healing studies to explore the effect of biomaterial or drug treatment. However, until today, to our knowledge, bone histomorphometry remain time-consuming and expensive. This incited us to set up an open-source freely available semi-automated solution to measure parameters like trabecular area, osteoid area, trabecular thickness, and osteoclast activity. Here in this study, the authors present the adaptation of Trainable Weka Segmentation plugin of ImageJ to allow fast evaluation of bone parameters (trabecular area, osteoid area) to diagnose bone related diseases. Also, ImageJ toolbox and plugins (BoneJ) were adapted to measure osteoclast activity, trabecular thickness, and trabecular separation. The optimized two different scripts are based on ImageJ, by providing simple user-interface and easy accessibility for biologists and clinicians. The scripts developed for bone histomorphometry can be optimized globally for other histological samples. The showed scripts will benefit the scientific community in histological evaluation.