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Abstract The dimensionless critical shear stress (τ*_c) needed for the onset of sediment motion is important for a range of studies from river restoration projects to landscape evolution calculations. Many studies simply assume aτ*_cvalue within the large range of scatter observed in gravel‐bedded rivers because direct field estimates are difficult to obtain. Informed choices of reach‐scaleτ*_cvalues could instead be obtained from force balance calculations that include particle‐scale bed structure and flow conditions. Particle‐scale bed structure is also difficult to measure, precluding wide adoption of such force‐balanceτ*_cvalues. Recent studies have demonstrated that bed grain size distributions (GSD) can be determined from detailed point clouds (e.g. using G3Point open‐source software). We build on these point cloud methods to introduce Pro+, software that estimates particle‐scale protrusion distributions andτ*_cfor each grain size and for the entire bed using a force‐balance model. We validated G3Point and Pro+ using two laboratory flume experiments with different grain size distributions and bed topographies. Commonly used definitions of protrusion may not produce representativeτ*_cdistributions, and Pro+ includes new protrusion definitions to better include flow and bed structure influences on particle mobility. The combined G3Point/Pro+ provided accurate grain size, protrusion andτ*_cdistributions with simple GSD calibration. The largest source of error in protrusion andτ*_cdistributions were from incorrect grain boundaries and grain locations in G3Point, and calibration of grain software beyond comparing GSD is likely needed. Pro+ can be coupled with grain identifying software and relatively easily obtainable data to provide informed estimates ofτ*_c. These could replace arbitrary choices ofτ*_cand potentially improve channel stability and sediment transport estimates.