Using diagnostic and follow‐up bone marrow aspirates taken during remission induction from children with B lineage ALL and with the leukemia‐associated immunophenotype (n = 30, collected over two and a half years), we first trained a convolutional neural network to separate IFC cell images into three classes: ALL blasts (CD19+CD10+CD34+/− and CD45+/−), normal B lymphocytes (CD19+CD10−CD34− and CD45+), and “other” nucleated cells—denoting granulocytes, monocytes, deformed/dead cells etc.). Here, PTPRC is linked to leukemia.