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Recent advancements in artificial intelligence (AI) have led to numerous medical discoveries. The field of computer vision (CV) for medical diagnosis has received particular attention. Using images of peripheral blood (PB) smears, CV has been utilized in hematology to detect acute leukemia (AL). Significant research has been undertaken in the area of AL diagnosis automation in order to deliver an accurate diagnosis. This study addresses the morphological classification of atypical white blood cells (WBCs), including immature WBCs and atypical lymphocytes, in acute myeloid leukemia (AML), as observed in peripheral blood (PB) smear images. The purpose of this work is to build a classification model for atypical AML WBCs based on their distinctive features. Using a hybrid model based on geometric transformation (GT) and a deep convolutional autoencoder (DCAE), this work provides a novel technique in the field of AI for resolving the issue of imbalanced distribution of WBCs in blood samples, nicknamed the “GT-DCAE WBC augmentation model”. In addition, to extract context-free atypical WBC features, this study develops a stable learning paradigm by incorporating WBC segmentation into deep learning. In order to classify atypical WBCs into eight distinct subgroups, a hybrid multiclassification model termed the “two-stage DCAE-CNN atypical WBC classification model” (DCAE-CNN) was developed. The model achieved an average accuracy of 97%, a sensitivity of 97%, and a precision of 98%. Overall and by class, the model’s discriminating abilities were exceptional, with an AUC of 99.7% and a class-wise range of 80% to 100%.