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Multispectral transillumination imaging is a promising modality for noninvasive imaging of living tissue. Multispectral Nevoscope imaging is directed toward the imaging of skin lesions for the detection and characterization of skin cancers through the volumetric analysis of selected chromophores, such as melanin, oxy-, and deoxyhemoglobin. In this letter, we present a novel method of recovering depth-dependent measurements from transillumination images obtained through the Nevoscope. A method for estimating the depth-dependent point spread function is presented and used in recovering multispectral transillumination images of a skin phantom or lesion through blind deconvolution. A method for ratiometric analysis for the quantification of oxy- and deoxyhemoglobin is then presented and evaluated on a skin phantom. The presented methods would allow reliable quantitative analysis of multispectral Nevoscope images for early detection of angiogenesis leading to early diagnosis of skin cancers.