The Molecular Pathology and Imaging Core (MPIC)

Research Resource Identifier: SCR_022420

The Molecular Pathology and Imaging Core is a resource for researchers at Penn, CHOP, and beyond.  We offer histological services, equipment, and technical expertise to assist in a variety of research projects.

We are located at 931-933 BRB II/III.  Please contact an MPIC team member if you have any questions or would like to submit an order.

MPIC is funded by the Center for Molecular Studies in Digestive and Liver Diseases (NIH P30 DK050306).

Grant Citation

Please cite the Center for Molecular Studies in Digestive and Liver Diseases (P30DK050306), as well as our Research Resource Identifier (RRID: SCR_022420) in all publications related to core usage.


Jonathan P. Katz, MD –

Core Personnel

Technical Director
Kate Bennett –

Research Specialist
Rebecca Ly –

Jem Palma -

Equipment Calendar

On-line Tissue Order Form

Histological Services

All costs are listed below.

  • Tissue Processing and Paraffin Embedding
  • Paraffin Sectioning
  • OCT/Frozen Sectioning
  • Staining
    • H&E
    • Alcian Blue
    • Oil Red O
    • PAS
    • Trichrome
  • Visium Spatial Transcriptomics - see 'Ordering and Pricing for details'


Training is available for all equipment.


No charge to members for reagents listed below:

  • Secondary Antibodies
    • Cy2/Alexa Fluor 488
      • Anti-Armenian Hamster
      • Anti-Chicken
      • Anti-Digoxigenin
      • Anti-Goat
      • Anti-Guinea Pig
      • Anti-Mouse
      • Anti-Rabbit
      • Anti-Rat
      • Anti-Sheep
    • Cy3
      • Anti-Armenian Hamster
      • Anti-Chicken
      • Anti-Digoxigenin
      • Anti-Goat
      • Anti-Human
      • Anti-Mouse
      • Anti-Rabbit
      • Anti-Rat
      • Anti-Sheep
      • Anti-Syrian Hamster
    • Cy5
      • Anti-Chicken
      • Anti-Goat
      • Anti-Guinea Pig
      • Anti-Mouse
      • Anti-Rabbit
      • Anti-Rat
      • Anti-Sheep
    • Biotinylated
      • Anti-Chicken
      • Anti-Goat
      • Anti-Guinea Pig
      • Anti-Hamster
      • Anti-Human
      • Anti-Mouse
      • Anti-Mouse
      • Anti-Rabbit
      • Anti-Rat
      • Anti-Sheep
      • Anti-Syrian Hamster
  • Kits
    • VectaStain Elite ABC kit (DAB reporter, Vector)
    • VectaStain Elite ABC kit (AP reporter, Vector)
    • Avidin / Biotin Blocking kit (Vector)
    • Peroxidase Substrate kit DAB (Vector)
  • Additional Reagents
    • DAPI
    • Propidium Iodide
    • Protein Blocker
    • Sudan Black B
    • YoYo

Consultation Services

CPC Pathologists will provide consultations for Center investigators.  Each consultation will involve up to a 30-minute review of select slides, comments on the findings, and recommendations on possible interpretations and follow-up experiments.

How to Submit Samples

Please place an order using our online tissue order form here.  Specimen IDs’ should be listed in vertical format with one ID per line.

Please create a Unique ID for each sample, 15 characters or less.  We batch process samples and are not responsible for mix-ups if there are duplicate identifiers between your samples and previously submitted samples, other lab members' samples, etc.  We recommend you label each sample with its unique ID on the front and side of the cassette, using either a pencil or a chemical-resistant pen.  

Samples should be pre-fixed in individual cassettes, then transferred to a container filled with 70% EtOH and labeled "PI's last name/Contact name” prior to drop off on the MPIC shelf in cold room 965.  It is difficult to return glassware so MPIC users are welcome to borrow a beaker. Paraffin blocks, slides, and slide boxes can also be placed on the MPIC shelf in cold room 965.

You will receive an email when your order is complete and ready to be picked up.

Please contact an MPIC staff member if you have any questions or concerns about submitting your order.

Molecular Pathology & Imaging Core Services are available at subsidized prices to AFCRI Members and Members of the Center for Molecular Studies in Digestive and Liver Diseases. Center Member Application (Word doc)


Center Members/AFCRI Members

UPENN and CHOP (Non-Center Members)
Rush Order (Completed within 1 week) 2x charge 2x charge
Tissue Processing and Embedding Only $5.00/block $7.50/block
Frozen or Paraffin Sectioning Only (Includes up to 7 Slides with 1 or 2 H&E) $17.50/block $26.25/block
Processing, Embedding, and Sectioning (Includes up to 7 Slides with 1 or 2 H&E) $22.50 /sample $33.75 /sample
Additional Sections $2.50/slide $3.75/slide
Additional H&E $2.50/slide $3.75/slide
Special Stains: PAS, Trichrome, Alcian Blue, Oil Red O $9.00/slide $14.00/slide
RNase-Free Sectioning Additional $2.50 / slide Additional $3.75/slide
Laser Capture Microscope Use $7/LCM collection tube $20/hour, and $7/LCM collection tube
Leica BOND RXm Use $6.00/slide $9.00/slide
X-Clarity Tissue Clearing System $20.00/day $30.00/day
Custom Services/Sectioning (Discuss in advance with MPIC staff) $140/hour  
Aperio Slide Scanner Use $50 / hour $75 / hour


Visium Services and Pricing:

Tissue processing:

Processing and embedding = $5/sample

Tissue Adhesion Test (performed on 4 blocks/samples)= $10/slide (with 1 sample per slide)

Visium Sectioning in RNAse free Conditions= $20/slide (up to 4 samples per slide)


$150 for widefield microscope training

$50 / hour for Center and AFCRI members

$75 / hour for CHOP, Penn, and Industry

OR MPIC can image at $140/hour


$140 (covers time and reagent costs) 

Decrosslinking, Permeabilization, etc.:

These steps are not covered by MPIC services and should be performed by the lab or in conjunction with a sequencing core (MPIC has been working closely with NGSC)


  • Fluorescent & Brightfield
    • Two Nikon E600 microscopes with Brightfield, Nomarski and Fluorescent optics. Z-series and deconvolution.
    • Nikon E600 equipped with Brightfield and Nomarski optics.
  • Widefield Fluorescent

    • Nikon Eclipse Ti-U microscope with environmental chamber and warming plate for live-cell imaging. Capable of imaging DAPI, FITC, Cy3, Cy5, and brightfield color with an automated stage. Equipped with image stitching capabilities and Metamorph software.
  • Laser Capture Microdissection
    • Nikon Eclipse TE2000-S with Brightfield, Phase Contrast, Fluorescent optics and imaging.
  • Inverted Leica DM IRB microscope with Brightfield, Phase Contrast and Fluorescent optics.
  • Dissecting Microscope
    • Nikon SMZ-U dissecting microscope with imaging.
    • Nikon SMZ645 dissecting stereo microscope can be signed out.
  • Slide Scanner
    • Leica Aperio Slide Scanner
    • Brightfield and Fluorescent Imaging, Z-Stack capabilities
    • Images can be viewed, annotated, etc with Leica's free software ImageScope
  • Leica BOND RXm Autostmatic slide stainer
  • X-Clarity Tissue Clearing System
  • Pressure Cooker
  • Snap Freezer
  • HybEZ II Hybridization Oven


  • Nikon NIS-Elements
  • iVision
  • Metamorph

Other Cores      

School of Medicine Cores

Educational Sites

Microscopy U - Extensive information about microscopy provided by Nikon
ImageJ User Guide - Helpful with learning to use ImageJ

Spectrum Viewers

Invitrogen Spectrum Viewer - Useful in determining the excitation and emission peaks of various fluorophores

Free Software

ImageJ - Imaging software provided by NIH.
Fiji - ImageJ with additional plug-ins

  • Developmental Biology 8th Edition, by Gilbert
  • Mouse Development: Patterning, Morphogenesis, and Organogenesis, by Rossant and Tam
  • The Anatomical Basis of Mouse Development, by Kaufman and Bard
  • Under the Microscope, by Curry
  • Advanced Laboratory Methods in Histology and Pathology, by Mikel
  • Laboratory Methods in Histotechnology, by Prophet, Mills, Arrington, Sobin
  • Techniques in Immunochemistry, by Bullock and Petrusz
  • Analytical Morphology: Theory, Applications & Protocols, by Gu
  • The Rat Brain, by Konig and Klippel
  • Histopathological Methods and Color Atlas of Special Stains and Tissue Artifacts, by Luna
  • Antibodies: A Laboratory Manual, by Lane and Harlow
  • Color Atlas of Basic Histology 2nd Edition, by Berman
  • Atlas of Histology with Functional Correlations 8th Edition, by Eroschenko
  • Tumors of the Intestines - Second Series, by Fenoglio-Preiser
  • Live Cell Imaging: A Laboratory Manual 2nd Edition, by Goldman and Spector
  • The Image Processing Handbook 4th Edition, by Russ
  • Fluorescence Microscopy 2nd Edition, by Herman
  • Handbook of Biological Confocal Microscopy 3rd Edition, by Pawley
  • Poly Scientific R&D Corp Reference Guide
  • Fundamentals of Light Microscopy and Electronic Imaging, by Douglas B. Murphy
  • Bancroft’s Theory and Practice of Histological Techniques 8th Edition, by Suvarna, Layton, Bancroft