A fully convolutional network (FCN) implemented on a specialized processor optimized for convolution computation can achieve a speed-up in cell classification. Without re-optimizing the specialized processor, a further speed-up is achieved by compacting a testing image of cells, and processing the compacted testing image with the FCN. The testing image is first segmented into a background and regions of interest (ROIs). The ROIs are packed closer together by rearranging the ROIs without resizing them under a constraint that any two adjacent rearranged ROIs are separated by a distance in pixel not less than a minimum distance determined according to stride values of FCN convolutional layers. Geometrical operations in ROI rearrangement include relocating the ROIs and, optionally, rotating the ROIs. The rearranged ROIs are enclosed by a boundary, typically a rectangular boundary, to form the compacted testing image having an area smaller than that of the testing image.