Independent subspace analysis (ISA) is used to learn (42) filter kernels for CLE images in brain tumor classification. Convolution (46) and stacking are used for unsupervised learning (44, 48) with ISA to derive the filter kernels. A classifier is trained (56) to classify CLE brain images based on features extracted using the filter kernels. The resulting filter kernels and trained classifier are used (60, 64) to assist in diagnosis of occurrence of brain tumors during or as part of neurosurgical resection. The classification may assist a physician in detecting whether CLE examined brain tissue is healthy or not and/or a type of tumor.