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Guide to using these images 
     This atlas contains microscopic images of immunofluorescent-stained intestinal tissues. At present, the atlas is primarily composed of normal human biopsies. Images are being added continuously, and include increasing numbers of diseased human biopsies. Over time, the atlas will be expanded to include a comparable set of biopsies from mice.
     Specific specimen sets can be found by searching, with the filter button, and making selections within each of the searchable fields. Each subject whose biopsies were used was assigned a unique identifier, making it possible to identify multiple biopsies from one individual. Each specimen was assigned a unique core number to simplify comparison of multiple stains of a single tissue. The biopsies were stained in groups as individual tissue microarrays (TMAs) named according to the primary site of tissues within the TMA. Tissues from other sites are included within each TMA as internal staining controls.  
     Clicking on the preview (thumbnail) image associated with a particular image will launch that image in OMERO PathViewer in a new window. Clicking the Viewing Options tab on the Browse window shows the stain used for each channel and allows modification of viewing properties, including color assignment and scaling (brightness and contrast). Because scaling has been applied to groups,of images broadly, it will likely be necessary to adjust scaling for individual images. This will not change pixel values, but will only affect the displayed values. Colors displayed for each channel can also be modified. One may also view the far red channel, which, in some cases, has an additional stain that can be useful in tissue orientation, e.g. ß-actin, using the viewing tab controls. This, like all of the channels, can be easily reassigned to a different display ciolor.
     Clicking on the eye icon to the left of the preview image provides additional details about the tissue. Clicking on the staining method icon will display details of the methods and reagents used to prepare the image shown. If all of the preview images fail to appear, please simply refresh your page (F5 in most PC browsers).
     We are currently working to develop tools to assess these biopsies quantitatively and to image cultured human intestinal stem cell monolayers.
     If you have suggestions or other comments, please feel free to contact Jerrold R. Turner 

Jerrold R. Turner, MD, PhD
Departments of Pathology
and Medicine (Gastroenterology)

Brigham and


NRB 730
77 Avenue Louis Pasteur
Boston, MA 02115