The Molecular Pathology and Imaging Core (MPIC)

The Molecular Pathology and Imaging Core is a resource for researchers at Penn, CHOP, and beyond. Located at 931-933 BRB II/III, we offer histological services, equipment, and technical expertise to assist in a variety of research projects. Please contact an MPIC team member if you have any questions.

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

Reserve equipment here: Equipment Calendar

Order histological services here: On-line Tissue Order Form

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

Core Personnel


Jonathan P. Katz, MD –

Technical Director

Kate Bennett –

Research Specialist

Rebecca Ly –

Jem Palma -


Histological Services

All costs are listed under ‘Ordering and Pricing’

  • Tissue Processing and Paraffin Embedding
  • FFPE Sectioning
  • Frozen Sectioning
  • RNase free Processing, Embedding, and Sectioning
  • Staining
    • H&E
    • Alcian Blue
    • Masson’s Trichrome
    • Oil Red O (not recommended for FFPE)
    • PAS
  • Visium & Xenium Spatial Transcriptomics


Training is available for all equipment. See ‘Equipment’ for further information


No charge to members for reagents listed below:

  • Secondary Antibodies
    • Cy2/Alexa Fluor 488
      • Bovine Anti-Digoxigenin
      • Donkey Anti-Goat
      • Donkey Anti-Guinea Pig
      • Donkey Anti-Mouse
      • Donkey Anti-Rabbit
      • Donkey Anti-Rat
      • Donkey Anti-Sheep
      • Goat Anti-Armenian Hamster
      • Mouse Anti-Chicken
    • Cy3
      • Anti-Digoxigenin
      • Bovine Anti-Goat
      • Donkey Anti-Chicken
      • Donkey Anti-Guinea Pig
      • Donkey Anti-Human
      • Donkey Anti-Mouse
      • Donkey Anti-Rabbit
      • Donkey Anti-Rat
      • Donkey Anti-Sheep
      • Goat Anti-Armenian Hamster
      • Goat Anti-Syrian Hamster
    • Cy5
      • Donkey Anti-Chicken
      • Donkey Anti-Goat
      • Donkey Anti-Guinea Pig
      • Donkey Anti-Mouse
      • Donkey Anti-Rabbit
      • Donkey Anti-Rat
      • Donkey Anti-Sheep
    • Biotinylated
      • Goat Anti-Chicken
      • Goat Anti-Guinea Pig
      • Goat Anti-Hamster
      • Goat Anti-Human
      • Goat Anti-Mouse
      • Goat Anti-Rabbit
      • Horse Anti-Goat
      • Horse Anti-Mouse
      • Rabbit Anti-Rat
      • Rabbit Anti-Sheep
  • 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 unique and listed in vertical format with one ID per line

Formalin Fixed Paraffin Embedded (FFPE)

  • Samples should be placed in individual histology cassettes that are labeled on the front and side with a unique Specimen ID in pencil
    • Chemical resistant marker is not recommended
    • All specimens sharing the same cassette will be embedded into the same block
    • Samples are batch processed and MPIC is not responsible for mix-ups due to duplicate identifiers between your samples and previously submitted samples, other lab members' samples, etc.  
    • Cassettes and biopsy sponges are provided free of charge and available in bay 931 for MPIC users
  • Samples should be properly fixed in 10% neutral buffered formalin (NBF), rinsed in PBS, and fully submerged in a beaker of 70% ethanol labeled with “PI’s last name/Contact Name”
    • MPIC users are welcome to borrow beakers from bay 933. We will try to return your glassware, but we recommend borrowing from us
  • Specialty tissue/processing:
    • Adipose tissue should be submitted in a separate beaker from other tissue types as it requires specific processing
    • Any tissue containing bone (sternum, spine, paws, etc.) should be properly decalcified prior to submission
  • All beakers with samples to be processed, paraffin blocks, slides, and slide boxes can be dropped off on the MPIC labeled shelf in cold room 965
  • With our standard 7 slides per sample, a large slide box can fit a maximum of 14 samples worth of slides. If providing slide boxes, please ensure a correct amount of slide boxes are dropped off to accommodate all your samples

Frozen Samples

  • Frozen samples should be embedded in the center of a disposable plastic base mold, labeled with a unique Specimen ID, and fully encapsulated in OCT
  • Frozen samples and slide boxes can be dropped off on the 3rd or 4th shelf of MPIC’s -80 C freezer across from cold room 965
    • Please do not put ice boxes or dry ice in the freezer
    • Separate slide boxes should be provided for frozen slides and stained slides


You will receive an email with pick-up instructions when your order is complete

  • Our standard turnaround time is 1-3 weeks with a rush turnaround time of 7 business days for double the standard rate
  • Our pick-up table is located opposite cold room 981 in the same hallway as the service elevator on the 9th floor of BRB

Please contact an MPIC staff member if you have any questions or concerns

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 7 business days)

2x charge

2x charge

Tissue Processing and Embedding Only



Frozen or Paraffin Sectioning Only (Includes up to 7 Slides with 1 or 2 H&E)



Processing, Embedding, and Sectioning (Includes up to 7 Slides with 1 or 2 H&E)

$22.50 /sample

$33.75 /sample

Additional Sections



Additional H&E



Special Stains: Alcian Blue, Masson’s Trichrome, Oil Red O, PAS



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



X-Clarity Tissue Clearing System



Custom Services/Sectioning (Discuss in advance with MPIC staff)



Aperio Slide Scanner Use

$50 / hour

$75 / hour


Visium Services and Pricing

Tissue processing

  • Processing and embedding = $5/sample
  • Visium Sectioning in RNase free Conditions = $20/slide (up to 4 samples per slide)


  • $50/hour for Center and AFCRI members
  • $75/hour for CHOP, Penn, and Industry
  • OR MPIC can image at $140/hour

H&E Staining:

  • $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)


Xenium Services and Pricing

MPIC offers a self-service Xenium Imager for you to conduct your own experiments on your own time. All reagents not sold by 10x Genomics will be provided by MPIC and are included in the daily fee. From now until December 31, 2023, email MPIC staff directly to schedule your Xenium run. More information regarding the launch of our Xenium booking calendar will be announced in the new year. 


  • Processing and embedding = $7.50/sample
  • Xenium Sectioning = $100/slide
  • $250/day for Center and AFCRI members
  • $500/day for CHOP, Penn, and Industry


  • Schedule: Email MPIC staff to book your Xenium run

  • Order with 10x: Place an order with 10x Genomics for your Xenium reagent kits if you haven't already

  • Order with MPIC: 

         - For FFPE: we offer processing, embedding, and sectioning of your fixed samples onto your Xenium slides

         - For FF: we offer sectioning of your already OCT embedded FF tissue onto your Xenium slides

         - For paraffin embedded blocks: we offer sectioning onto your Xenium slides

  • Xenium Day 1: MPIC staff will conduct Xenium training followed by benchwork 

  • Xenium Day 2: Benchwork followed by the loading and running of the Xenium (2-4 days)

  • Xenium Day 3 (when run is complete): Post-run cleanup, unload Xenium, collect data

  • Optional post-run H&E: Email MPIC staff to book your optional post-run H&E

Reserve equipment here: Equipment Calendar



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


Spatial Biology Equipment

  • Visium CytAssist
  • Xenium In Situ
    • MPIC also has a C1000 Touch Thermocycler, the recommended model by 10x Genomics for their spatial biology assays


Other Equipment

  • Leica BOND RXm Automatic slide stainer (IHC and IF staining)
  • X-Clarity Tissue Clearing System
  • Pressure Cooker
  • Snap Freezer
  • HybEZ II Hybridization Oven
  • Cryostat Microm HM 505 E


  • 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