Scanning/TMA – Oncology Tissue and Imaging Services

Digitally Scanned Slide Storage Policy

The TMA Core at Johns Hopkins is a University Service Center/Shared Resource that is part of the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and the Department of Pathology.

The TMA Core has constructed over 850 TMAs for over 50 investigators containing ~96,000 tissue cores from tumors from the prostate, breast, pancreas, gall bladder, cervix, ovary, brain, liver, urinary bladder, salivary glands, esophagus, head and neck, thyroid and various cell lines. Users have published over 150 manuscripts involving Johns Hopkins University TMAs.

Instrumentation is available to automatically capture high resolution digital images of TMA spots and perform semi-automated quantitative image analysis. Users have access to a set of Open Source and Aperio web-based software tools and backend database (TMAJ) that were developed to facilitate the all facets of research involving TMA technology from TMA design, data entry, image diagnosis, analysis, and publishing on the Internet. Recently we have incorporated comprehensive histology services into the TMA core by moving the Oncology Histology Lab into the TMA lab space. Also, we have incorporated immunohistochemistry and fluorescence in situ hybridization services into the TMA Core.

Digital Image Storage Policy

The TMA Core Facility does not currently charge users for storage of scanned whole slide images on our Spectrum server. Our current policy is to retain all compressed whole slide image files for a minimum of 5 years from the time they were scanned. The core will not provide any long term storage for uncompressed whole slide image files. Although best practices are followed to prevent loss of user data, the TMA Core Facility makes no guarantees about the accessibility or integrity of user data and accepts no responsibility for damages of penalties that result from data loss. If your digital scans are critical to your research projects, it is advised to request DVDs or provide an external hard drive to which the core can transfer your files. The TMA Core Facility reserves the right to delete any whole slide image files older than 5 years and to modify this digital image storage policy.

Imaging and Image Analysis of Tissue Microarrays (pdf)
Requirements for Good Tissue Microarray (TMA) Results (pdf)

TMAJ Software Project

For inquires or registering, please contact:

Kristen Lecksell – call 410-502-7452
Tracy Jones – call 717-817-1625

Company Location:

Sheikh Zayed Tower – M2101
1800 Orleans Street
Baltimore, MD. 21231

Scanning and TMA Services

We can scan your whole standard slides or tissue microarray slides.
Benefits of whole slide scanning include:

Save hours of time by not having to take photomicrographs of your slides with a digital camera.
Publication quality bright field images at any magnification up to 40X.
Free Web-based viewing software – OTS Web Storage.
Automated TMA segmentation for highthroughput IHC analysis.

QA Policy – Effective 6/26/14

In order to improve our throughput and reduce the turnaround time for scanning, standard histology slides scanned at 20x or 40x will no longer receive additional manual QA after the run. If you are unhappy with a scan on a slide in this category, please return it and we will rescan it free of charge.

For $1 more/slide we will QA your slides, if requested. See “Services, Request, and Prices” for Scanning and TMA cost.

How to Effectively PREP-Clean Slides for Scanning

Video 1: Cleaning slide with alcohol

Video 2: Shave excess labels from slide

Video 3: Remove excess mounting media from slide