Protocol for isotype-resolved 3D imaging and quantification of bone marrow plasma cells in murine femurs.

Bone marrow plasma cells maintain durable antibody responses, but their tissue localization and morphology are difficult to quantify in situ. Here, we present a protocol for isotype-resolved 3D imaging and quantification of bone marrow plasma cells in murine femurs. We describe steps for fixation, optimal cutting temperature (OCT) coumpound embedding, longitudinal opening of mouse femurs, whole-mount immunostaining, optical clearing, and confocal 2D/3D imaging. We detail an Imaris-based workflow for reproducible single-cell segmentation, isotype-resolved counting, and the extraction of morphological features from defined regions of interest.