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The cottonseed delinting removes lint from the seed coat to improve plantability and maintain the seed's physiological quality, therefore, this work aimed to determine the effect of delinting and neutralizers' residual on the physiological quality of stored cottonseed by using image analysis phenotyping. The experiment was a randomized factorial design of 3 x 4 x 2 and two periods of storage evaluation (0 and 180 days). The cotton seeds were delinted at three different times (2, 4, and 10 minutes), neutralized using four distinct neutralizers (Quicklime, Hydrated lime, Filler lime, and NaOH), and there were seeds with and without neutralizer residue. The evaluations carried out were: water content, seed residual lint imaging, germination, seedling emergence, and seedling length imaging. The neutralizers Quicklime, Hydrated lime, and Filler lime do not need removal from the cotton seed coat. In storage, only the neutralizer NaOH has a high latent effect in lowering cottonseed quality, and the other neutralizers have lower physiological quality when the residue is removed. The image analysis phenotyping is efficient in identifying seedlings' vigor. [ABSTRACT FROM AUTHOR]