Whole Slide Scanning and Analysis

Location: Thomas Building, DE-512
Contact phone: (206) 667-4205
Contact e-mail: imaging@fredhutch.org

Whole slide scanning and analysis (digital pathology) allows researchers to scan large specimens such as whole tissue sections, whole slides, and tissue micro array slides (TMAs) for archival, sharing, and analysis purposes. The acquired high resolution images provide a visual record that can be archived or shared with collaborators for evaluation and analysis. The images can also be processed via dedicated image cytometry software for unbiased quantitative analysis (scoring). The resource provides microscopy equipment for automated slide imaging (Tissuefax system), and TissueQuest and Histoquest software for scoring slides stained with immunohistochemical (H&E, DAB) or immunofluorescent methods.

Transmitted light image of whole mouse brain section acquired with 10x objective through automated image stitching (left), and full resolution detail (right).

Transmitted light image - mouse brain section. Image stitching (left), full resolution detail (right).


(For technical details, follow the links to individual instruments or software below.)

Tissuegnostics Tissuefax system.he Tissuefax is an automated microscope for the imaging of histology slides, including large tissue sections and tissue micro-array (TMA) slides.

Recommended Uses: imaging of histology slides including smears, cytospins, and whole tissue sections. Imaging of tissue micro-array (TMA) slides. Slide digitization and archival; digital pathology; quantitation and scoring of IHC and IF staining.

Tissuegnostics TissueQuest software: Image cytometry software for the semi-automated analysis of fluorescent images acquired on the Tissuefax system.

Tissuegnostics HistoQuest software: Image cytometry software for the semi-automated analysis of immunohistochemistry images acquired on the Tissuefax system.

Scheduling time for instruments, training, and support:

To schedule time on any of our microscopes, or to schedule staff assistance or training, please use iLab. The resource is open to all from 9:00 AM - 5:00 PM, Monday through Friday. After hours access can be granted to experienced users and requires training by the resource's staff. Please contact Scientific Imaging for further details.

How to access your data:

Data acquired on Scientific Imaging instruments is transferred to the si folder in the user's fred account. If you do not have a fred account, please submit the computing account application form. Once you have obtained a fred account, please contact Scientific Imaging so that we can create an si link for you. External users without access to fred can obtain their data via ftp, or can download to their own data storage device from one of our dedicated computers. Please note that no portable drives are allowed on instrument computers.