mcb probe generation workflow, applicable to other species as well. I Murine metaphase stained with Giemsa. All chromosomes from this metaphase were dissected one by one and collected into separate micropipettes. Original amplification based on a single chromosome template resulted in proto-wcp probes. II Generation of murine wcp probes and their attribution. “Doubles” corresponding to the same pair of homologue chromosomes were excluded by several rounds of co-hybridization (A). Chromosome-specific libraries were assigned by co-hybridization with available BAC probes (B), available murine pcp probes (D), or by applying them onto metaphase spreads of WMP2 cell line (C). III Generation of murine pcp paints and their incorporation into mcb probe mixes. Here, reverse-FISH of the pcp from murine chromosome 9 corresponds to FISH-MD experiment in Additional file 1: Video 1. Fluorochrome profile and pseudocolor banding pattern resulting after application of murine mcb 9.