At NYU Langone’s Experimental Pathology Research Laboratory, our experts use advanced technologies to perform in-house services such as tissue preparation, embedding, sectioning, histochemical staining and immunohistochemistry, antibody optimization and validation, digital whole-slide scanning, laser capture microscopy, and image analysis.

Additionally, many of our state-of-the-art instruments are available for rental through iLab (review login instructions), our web-based scheduling, ordering, and billing system, including instruments for embedding, sectioning, imaging, and laser capture microscopy.

We provide consultation and guidance to help you plan complex experiments, as well as informal training for standard procedures and instrument rental. If this is your first time working with us, please contact Cynthia Loomis, MD, PhD, director, at cindy.loomis@nyulangone.org.

Histology

All histology technologies are performed on-site with an average turnaround time of 5 to 15 working days, depending on the size and complexity of the project.

Tissue Preparation

The Experimental Pathology Research Laboratory has two automated high-throughput processors for paraffin processing of animal tissues. We also offer cryopreservation and preprocessing support, including perfusion and immersion fixation, decalcification, basic tissue grossing, and cassetting.

Embedding

Paraffin embedding, cryoembedding, and agarose embedding technologies are available for animal tissues. Cryoembedding is performed using a liquid nitrogen–chilled isopentane bath to ensure minimal ice crystal formation. Cryoembedding tools, as well as our animal paraffin embedders, are available for rental.

Sectioning

Our experts offer paraffin sectioning, frozen sectioning (fixed or fresh), and vibratome sectioning. Sections can be stained or prepared for downstream DNA, RNA, or protein extraction and analysis, if desired. We also offer nondecalcified bone cryosectioning using a modified Kawamoto cryofilm method. Our microtomes and cryostats are available for rental.

Histochemical Stains

Staining is performed on-site. In addition to standard hematoxylin and eosin staining, we offer more than 25 special histological stains, including trichrome, oil red O, picrosirius red, and others.

Spatial Profiling High Parameter High Resolution Technologies

We provide multiplex (up to six antibodies) and high-plex immunostaining using several technologies that include: tyramide signal amplification (Opal Akoya Biosciences), Co-detection by indexing (CODEX, Phenocycler Fusion; Akoya Biosciences) and barcoded antibody readout (GeoMx, CosMx, Nanostring).

Low parameter high throughput

These are experiments that require low (up to 6 antibodies or 4 gene transcripts) number of antibodies or RNA/DNA targeting probes and may or may not high volume. Our experts offer extensive options for routine and special immunohistochemical labeling, including standard chromogenic, immunohistochemistry, and up to seven-color multiplex immunofluorescence. We use manual labeling as well as automated high-throughput instruments. Our lab uses a standardized approach to optimize antibodies. Tissue samples are tested under a variety of conditions and treatments with the goal of producing high signal-to-noise performance for the assay. We maintain a database of all antibodies, conditions and runs performed in our laboratory.

RNA and Protein: High Parameter High Resolution Technologies

Experimental Pathology offers several modalities of spatial profiling of gene transcript and protein detection with antibodies.

For RNA analysis we offer three systems to evaluate gene expression in situ with subcellular resolution. We run CosMx (NanoString) and Xenium (10X). Additionally, we provide access to run and collect data on the MerScope (Vizgen). All three assays are based on binding of cDNA probes containing tags for cyclic fluorophore binding and releasing which create a code in situ [Chen, K et al]. Please reach out to ExpPath personnel for more information and experimental design.
 
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).

Whole Transcriptome Profiling Technologies

ExpPath routinely runs Visium (10X) (FFPE and frozen tissue) experiments and also offers Visium HD. We perform GeoMx whole transcriptome and protein profiling on FFPE specimens both technologies are performed in collaboration with the Genome Technology Center using Illumina NGS readouts.

Digital Imaging

ExPath provides brightfield digital pathology scanning, fluorescent whole slide and advanced multispectral while slide scanning.

Whole-Slide Scanning

We provide high-resolution digital whole-slide scanning for both brightfield and fluorescence systems using up to four colors. Whole slide scanning can be done in either of these three instruments: Nanozoomer (Hamamatsu), Leica AT2 (Leica Biosystems) and Phenoimager-HT (Akoya biosciences). Additionally, our other platforms (Phenocycler-Fusion, GeoMx DSP, CosMx, MerScope and Xenium) produce image data for hi-plex protein and gene profiling. All images are uploaded and available for viewing, annotating and sharing through OMERO Plus (Glencoe Software).

Image Data Support

ExpPath offers rental access and training to HALO AI (Indica Labs).
We can also run image analysis using HALO AI or Visiopharm for a specific project. For more information, please reach out to us.

In collaboration with Medical Center Information and Technology, ExpPath uses OMERO Plus (Glencoe Software) in an effort to promote data sharing while ensuring rigor and reproducibility. Most research image formats can be stored viewed and annotated in OMERO (in their native formats) through a web browser interface that can be accessed by any team member. Any laboratory can use OMERO Plus to manage their image data. ExpPath
provides training and support for this platform.

Fees

All technologies and instrument rentals are available to investigators at competitive prices.

The components of pricing for each technology includes the cost of consumables, the cost for technician time, and a percentage of any associated service contracts. As with many of our technologies, the incremental cost of each procedure is affected by overall volume. As volume increases, we pass the resulting savings on to users in the form of reduced prices.

If we are extremely busy and cannot readily expedite your project without disrupting our queue, a rush surcharge is applied. Please note that rush surcharge is double the price of all technologies.

Prices are subject to change. For details about pricing, parties are encouraged to contact us at exppath@nyulangone.org.