Translational Pathology Shared Resource


TPSR Sample Drop-Off and Pick-Up procedures:

We strongly suggest our users set up a consultation meeting if you are our first-time clients or before harvesting/sampling for a new project. We will review and discuss the sample collection and preparation procedures/protocols to ensure the best outcome for your precious samples: which will both properly illustrate the desired features of the anatomical, histopathological details and be compatible with your scientific research object as well as future analysis.  This initial remote or in-person consultation is free of charge to our clients.

For routine requests, such as fixed tissue samples for paraffin processing, embedding, sectioning, H&E stain and Special Stain; paraffin blocks for sectioning and staining; paraffin slides for staining; whole slides scanning, etc., walk-in drop-off/pick-up are welcome during our work hours (Mon-Fri, 8:15 am to 4:45 pm). 

For Equipment Reservations, Training/Consultation Requests, Frozen Requests as well as IHC/ISH Requests, please contact the Shared Resource (Tel: 215-503-3858/215-503-8826 or Email to schedule an appointment with this shared resource. 

When dropping off:

  • Please label request ID and/or name of the client on the sample container(s)/package.
  • Please print out the hardcopy of your request sheet and submit it together with other materials.
  • Please talk to one of our staff when dropping off samples, so we can check the samples and request details, safely store/secure the submitted materials, verify and update your request status.

PLEASE NEVER-EVER drop off samples without notifying our staff. Unnotified materials left for this laboratory might jeopardize the research request/project.


Important Information about Aperio CS2 ScanScope Brightfield Slide Scanning Service

Below are requirements and suggestions for you to utilize this service:

  1. As we upgraded the eSlideManager to the latest version, you will also need upgrade the image viewing software, ImageScope, to latest version (version or newer). Otherwise, there will be some difficulties when opening images from the new server.
  • To upgrade your personal PC, please uninstall the old version, download the latest version software through Leica official website and install it on your personal PC. You will be asked to register before downloading the software.
  • If you need upgrade the ImageScope software on your lab PC, please download the software from link above to your PC desktop in advance, and then submit a service request to Jeff IS&T solution center: under REQUEST SOMETHING\OTHER\ Other Request:

In “Describe what you need” area, tell Jeff IS&T that you need uninstall old version ImageScope software in your PC (Include the PCS# of on the Jeff IS&T service tag attached to the PC) and install the latest version (version of ImageScope software. Mention that the software was downloaded and saved on desktop.

  1. Your Aperio eSlideManager account login information and service request procedure will remain the same as before, but the server address to access your digital images is changed to: add this page to your favorites)
  2. Please contact this shared resource if you have any questions regarding this service.
  3. If you are new to the Aperio ScanScope System and would like to utilize this service, please contact this shared resource to register yourself in our system and initialize a training secession for the software.


About us:

The Translational Pathology Shared Resource provides full range, state of the art, detail-orientated, outstanding array of experimental histopathology services complemented by molecular pathology, digital pathology and veterinary hematology services to SKCC members, TJU and local research community in the greater Philadelphia area. In collaboration with our internal labs at TJU, we also facilitate the interactions between investigators and SKCC Biorepository and Pathology Department to access human tissue samples and perform Laser Capture Microdissection of tissues to capture individual cells. The Translational Pathology Shared Resource is used by over one hundred principal investigators and has provided key data that support many publications and grant applications.

Our Instruments



The mission of this shared resource is to provide:

  1. Full range outstanding array of experimental histopathology services, including paraffin and frozen tissue processing, slide preparation, histochemical staining (H&E and Special Stains)

  2. Immunohistochemistry (IHC) staining, which is performed on paraffin sections, frozen tissue or cytological preparations and utilizes a broad range of optimized commercial antibodies or antibodies provided by the investigator with automatic staining platform: DAKO Autostainer Plus and Biocare Medical IntelliPATH FLX®.

  3. TUNEL Labelling and in situ Hybridization using RNAscope® technique

  4. Light field whole slides scanning (20X and 40X) with Aperio CS2 ScanScope. Link to our Image server: SKCC TPSR eSlideManager Server Link

Procedures to Utilize This Shared Resource:

For all first-time users, please watch iLab user tutorials videos.

The procedures are:

1. Both PI and lab members who plan to use SKCC shared resources under iLab need to register in the iLab system.

2. Internal users will use their Jefferson campus credentials to log in after they register in the system.

3. External users can generate their own username and password. PI should register first, so their lab member can register under the PI’s lab.

4. Both internal and external PIs need to review and accept/approve the lab member’s membership request in iLab system before s/he can join and utilize the iLab portal.

See instruction: How to manage membership request and charge codes (for PI) 

See iLab registration link:

5. For internal users, PI needs to set up payment information with our IT expert Ryan Smalley (Tel: 3-9692, Email: after the registration. 

6. For external users, please generate a PO (Purchase Order) before submitting the request to us.

    No request will go through the iLab system to us without payment information.

7. For internal users, PI needs to assign a charge code to their lab members to allow them to access the charge code. See instruction How to manage membership request and charge codes (for PI)

8. After PI assigns the charge code, the lab member can submit a request to us in the iLab portal under Request Service tab. 

a. When filling out the 'Describe Work Requested in FULL DETAIL', please include at a minimum the following information, and consider adding other key relevant information:

    • Description of the Submitted Materials: such as species, organ/tissue type, fixative type and duration, current solution samples are stored in, etc.;
    • Trimming/Grossing and/or any Special Handling Requirements;
    • Processing and Embedding Requirement: such as oversized tissues need longer program to process, special embedding and/or sectioning orientation, etc.;
    • Sectioning Requirement: number of slides/sample, number of sections/slides, thickness of the section (our default thickness is 4 µm; cut into different levels, etc.;
    • Staining Requirement: Routine H&E, special stain, IHC, ISH, TUNEL, Multiplex staining, etc.;
    • Digital Scanning Requirement: 20X or 40X, attach sample information collection form if available;
    • Any additional requirements were not mentioned above.

b. Enter the sample "label” in the request form:

    • The label will show up on your slides. Please make sure labels on request form match labels on cassettes.
    • Type in material type or select from the drop-down menu. Drag to fill in the rest area if the material type is the same. The operation of this form is similar to Excel worksheet.

c. Enter the Charge Code or Purchase Order under payment information.

d. Check all information entered above to make sure it is correct.

e. Click Submit button to submit the request to this shared resource if you are ready to submit the request. Otherwise, click "save draft of form" at the end of "Forms and Request Details" to save it under your account.

f. Use the printer icon"" under "Forms and Request Details" to download a PDF file and print it out.

g. Please submit the request sheet together with the samples to us.

9. For Equipment Reservation, Training/Consultation Request, CBC Analysis request, Frozen Request as well as IHC/ISH Request, please always call 215-503-3858/8826 or email us to schedule an appointment before submitting the samples/request to this shared resource.

10. No appointment is needed for submitting samples for routine paraffin processing or paraffin blocks. 

11. We will review, update and confirm the request details with users and process the request once we have received the hard copy of the request sheet and all related materials.

12. Once we complete the request and update the request status to "completed", an automatic email (from: titled "NOTIFICATION: XXXX The Service request TR/PSR-XX-XXXX has been completed") will be sent out to you. This means you can come and pick up your completed work during our work hours, no appointment is needed unless there is temperature- and/or time sensitive materials involved.


Hallgeir Rui, MD, PhD | Director

Haifeng Yang, PhD | Co-Director

Zhijiu Zhong, MD | Laboratory Manager

Hours of Operation, Location and Telephone


8:30 AM - 4:30 PM

Monday - Friday except Holidays


233 S. 10th Street
Room 815, Bluemle Life Sciences Building       
Philadelphia, PA 19107




Useful Links and Resources

  1. iLab user tutorials videos

  2. How to manage membership request and charge codes(for PI)

  3. SKCC Translational Research Shared Resource - List of Services & Price Schedule

  4. Sidney Kimmel Cancer Center Shared Resources

  5. Sample preparation instruction for paraffin embedding

  6. Sample preparation instruction for frozen embedding

  7. Preparing Gel Block from Cell Lines or Cell Suspensions

  8. Aperio eSlideManager Server

  9. Policy for Aperio CS2 Digital Slide Scanning and Access of the eSlide Manager

  10. Aperio eSlide Manager User Account Request Form 

  11. Aperio CS2 Digital Image Scanning Sample Information Collection Form

  12. Aperio eSlideManager Operator Guide

  13. Aperio ImageScope User Guide

  14. Aperio WebScope User Guide

  15. Revised guides for organ sampling and trimming in rats and mice: Parts 1 – 3(A joint publication of the RITA and NACAD groups)

  16. The Internet Pathology Laboratory for Medical Education (Hosted By University of Utah Eccles Health Sciences Library)

  17. The Human Protein Atlas

  18. Sidney Kimmel Cancer Center


Name Role Phone Email Location
Hallgeir Rui, MD, PhD
(215) 503-9881
Bluemle Life Sciences Building, Rm 1008
Haifeng Yang, PhD
(215) 503-6163
Jefferson Alumni Hall, 336D
Zhijiu Zhong, MD, MS
Laboratory Manager
(215) 503-3858/8826/2237
Bluemle Life Sciences Building, Rm 815
Natalie Dougherty, MS
Research Assistant III
(215) 503-3858/8826/2237
Bluemle Life Sciences Building, Rm 815
Ruiyan Jing, BA
Research Assistant I
(215) 503-3858/8826/2237
Bluemle Life Sciences Building, Rm 815