[Objective] The major objectives of the experiment is to develop protocols of seedling image analysis to evaluate characteristics related to tolerance to deep sowing under dry direct sowing condition in rice. [Methods] Seeds of eighteen rice varieties with varied mesocotyl elongation and barnyard grass, crab grass were used in sand culture with 5 sowing depths of 3cm, 5cm, 7cm, 9cm, and 11cm. Seedling emergence was recorded each day. Digital images of seedling were obtained 15 days after sowing (DAS), and used to measure phenotypic parameters related to seedling growth based on image analysis. [Results] The protocol of image analysis is effective to obtain mesocotyl length and total leaf projected area simultaneously. Under 3cm sowing depth, seedlings of rice varieties without mesocotyl elongation were able to emerge on 6 DAS while seedlings with elongated mesocotyl emerged on 5 DAS. Under 5-7cm sowing depth, rice varieties without mesocotyl elongation failed to emerge while varieties with elongated mesocotyl delivered emerged seedlings on 7-10 DAS. The total leaf projected areas of 15 DAS seedlings were higher in varieties with mesocotyl elongation than varieties with short mesocotyl under same sowing depth. The differences were very noticeable under 7cm or higher sowing depths. Mesocotyl elongation was observed in both barnyard grass and crab grass seedlings that led to seedling emergence from 5cm and 3cm sowing depth, respectively. [Conclusion] Phenotyping protocol was developed to evaluated deep-sowing tolerance related parameters based on seedling image analysis. Mesocotyl length and total leaf projected area were measured after recognition of different parts like mesocotyl and leaves of the seedlings. Investigation on representative rice varieties and grass weeds indicated the key role of mesocotyl elongation on quick, uniform seedling emergence after deep sowing, and the early development of autotrophic capacity.