There is a growing need for exploring new sample cleaning and egg counting methods for plant-parasitic nematodes. Here, a better sample cleaning method is proposed, using an OptiPrep™ gradient density medium, while two semi-automatic egg counting methods which utilize custom software to automatically count the eggs are also discussed. The first counting method is a scanner imaging-based method and second is a lensless imaging-based method. A full, in depth, analysis of our sample cleaning method was conducted to calculate the egg recovery rates for different densities of the OptiPrep™ density gradient medium. A comparison of this egg recovery rate and that of the traditional sucrose-based method was also performed. The scanner counting method is simple and achieves accurate counts. While the lensless counting method uses flow cytometry and allows for the recovery of the eggs following the counting process. This method also works for unstained eggs which is essential for experiments where the viability of the eggs is important as the staining process often kills the organisms.