The difference can be found by looking at the particular filename, where files with “TS#” or “BS#”, where # is an integer, is a frozen slide, like this: The TCGA has both types of slides available, so care must be taken to obtain the correct cohort and * not* mix cohorts unless specifically part of your experimental design. It has a much nicer appearance, making it more amenable to computational analysis:Ī more full discussion is available here and here. Flash freezing is a fast and “easy” process, but frequently leaves the tissue damaged, giving it a swiss cheese type appearance:įFPE slides are the gold standard for diagnostic medicine, and are generated by fixing a specimen in formaldehyde and then embedding it in a paraffin wax block for cutting. Flash frozen samples are typically produced during surgery in a cryolab to help the surgeon determine if the borders of the tumor are clean( i.e., has the tumor been fully resected). This post discusses how to download the Formalin-Fixed Paraffin-Embedded (FFPE) slides for corresponding patients.įirst a brief introduction, the TCGA offers two types of slides, flash frozen and Formalin-Fixed Paraffin-Embedded (FFPE).

While there are a large number of images available in The Cancer Genome Atlas (TCGA), the ones which are currently available in the data portal are frozen specimens and are *not* suitable for computational analysis. Digital pathology image analysis requires high quality input images.

Tissue slide images svs