Frequently Asked Questions
Everything you need to know about working with IMCO — from getting started and sample requirements, to the specifics of each assay we offer. Can't find your answer here? Reach out and our scientific team will help.
Frequently Asked Questions
Answers to common questions about working with IMCO — from getting started and sample requirements to pricing, timelines, and data handling.
IMCO — the Immune Monitoring and Cancer Omics Labs — is a service laboratory of the OHSU Knight Cancer Institute that provides translational and immune-monitoring assays for academic investigators, biotech and pharmaceutical sponsors, and clinical trial teams. We support studies from early discovery through correlative analysis of clinical trial specimens, offering everything from single-marker IHC to spatial multiplex imaging, proteomics, and sequencing.
Reach out through the "Schedule a Consultation" link on our site or contact our team directly with a short description of your research question, sample types, and study timeline. A scientific lead will follow up to discuss feasibility, recommend an assay approach, and provide a scope of work and cost estimate before any samples are shipped.
We routinely work with formalin-fixed paraffin-embedded (FFPE) tissue blocks and slides, fresh or frozen tissue, whole blood, PBMCs, serum and plasma, and other biofluids. Sample requirements (fixation, minimum quantity, storage conditions) vary by assay, and our team will confirm specifications during project scoping.
Yes. While we are part of the OHSU Knight Cancer Institute, we regularly support external academic collaborators, biotechnology companies, and pharmaceutical sponsors on a fee-for-service basis. Many of our platforms are available under GLP-like or research-use-only workflows depending on the study's regulatory needs.
Pricing depends on the assay, panel size, sample number, and any custom analytics or reporting requested. After an initial consultation, we provide a written quote and scope of work outlining deliverables, turnaround time, and cost per sample so you can budget accurately before committing.
Turnaround varies by assay complexity, ranging from roughly two to three weeks for smaller, established panels to six to ten weeks for large cohort studies, custom assay development, or sequencing projects requiring extensive bioinformatics. We provide a project-specific timeline as part of every scope of work.
Absolutely — this is one of the most valuable parts of working with us. Our scientific leads regularly help investigators translate a biological question into an appropriate combination of assays, panel design, and sample size, drawing on experience across immunophenotyping, spatial biology, proteomics, and genomics.
Deliverables typically include raw and analysis-ready datasets, summary statistical reports, and custom figures or visualizations tailored to your study endpoints. Data are transferred through secure, access-controlled channels, and our team is available to walk through results and discuss interpretation.
All specimens and data are handled in accordance with OHSU's institutional policies and applicable regulations, including HIPAA where relevant. Samples are typically received and processed using de-identified or coded identifiers, and data are stored and transferred through secure, access-controlled systems.
Yes, and we frequently do. Many studies benefit from a multi-platform approach — for example, pairing spatial imaging with proteomic profiling and bulk sequencing on the same cohort. Our team can help sequence experiments across platforms so that tissue and sample volumes are used efficiently and results are complementary.
Turning high-dimensional data into decisions
Questions about our Visiopharm-powered image analysis, quantitative tissue analytics, and custom scientific reporting.
Research Analytics is our data interpretation and image analysis service, layered on top of assays such as spatial imaging, IHC, and flow-based platforms. Rather than delivering only raw images or files, we apply quantitative analysis so you receive interpretable, publication-ready data and figures.
Visiopharm is an industry-leading digital pathology and image analysis platform. As a Visiopharm technology partner, IMCO uses it to perform AI-assisted image analysis, quantitative tissue phenotyping, and spatial biology analytics with validated, reproducible algorithms rather than fully manual scoring.
In many cases, yes. If your images were generated on a compatible platform and meet resolution and file-format requirements, our team can evaluate whether they are suitable for analysis. Send us example files during project scoping and we'll confirm compatibility.
Typical deliverables include analysis-ready datasets (e.g., cell counts, marker positivity, spatial metrics), statistical summary reports, and custom visualizations and figures suitable for manuscripts or presentations. Exact outputs are defined during scoping based on your study endpoints.
Both. For common endpoints we apply validated, standardized workflows for efficiency and reproducibility. For novel questions or unusual tissue morphology, our analysts can develop and validate custom classifiers and quantification algorithms tailored to your samples.
Beyond Visiopharm, our analysts work in Python for custom data processing, FlowSOM and Cytobank for high-dimensional clustering, and GraphPad Prism for statistical testing and figure generation, allowing us to match the tool to the analytical question.
Yes, this is one of our core applications. We regularly support correlative analysis of clinical trial biospecimens, including custom cohort comparisons, biomarker discovery studies, and endpoint-specific reporting that aligns with a trial's statistical analysis plan.
Algorithms are validated against ground-truth or pathologist-reviewed regions before being applied to a full cohort, and quality-control checks are built into each analysis pipeline. Where relevant, a subset of results is cross-checked by a second analyst or reviewing pathologist.
Yes — a sample Research Analytics report is available to review so you can see the format and level of detail we provide. Ask your scientific lead for the current example report during your consultation.
It can be used either way. Many clients bundle analytics with an assay such as CycIF, GeoMx, or multiplex IHC, but the analytics team can also work as a standalone service on images or datasets you already have.
Single-cell resolution, tissue-wide context
Questions about cyclic immunofluorescence, high-plex spatial imaging, and our Lunaphore-powered workflow.
Cyclic Immunofluorescence (CycIF) is a spatial biology technique that allows dozens of protein markers to be visualized on a single tissue section through iterative rounds of staining, imaging, and signal removal. Unlike standard IHC, which is typically limited to one or a few markers per slide, CycIF preserves single-cell resolution while capturing a much broader, tissue-wide picture of the immune and tumor microenvironment.
Panel size depends on tissue quality and study design, but our CycIF workflow is built to support highly multiplexed panels well beyond what conventional chromogenic IHC can achieve, enabling comprehensive phenotyping of immune, stromal, and tumor cell populations within their native spatial context.
CycIF is typically performed on FFPE tissue sections, and works well with a wide range of tumor and non-tumor tissue types. Tissue integrity and section quality are important for successful multi-cycle staining, so our team reviews sample suitability early in project planning.
Lunaphore is our partner platform provider for spatial biology, supplying automated instrumentation that streamlines the iterative staining and imaging cycles required for high-plex spatial immunofluorescence. This automation improves consistency and throughput compared to fully manual multi-cycle staining.
Yes. CycIF is well suited to being paired with platforms like GeoMx digital spatial profiling or downstream sequencing, allowing investigators to correlate high-resolution single-cell spatial data with region-specific transcriptomic or proteomic information from the same tissue.
Because CycIF captures whole-slide or large tissue-region data rather than isolated fields, it preserves the broader architecture of the tumor microenvironment — including immune cell infiltration patterns, tertiary lymphoid structures, and spatial relationships between cell populations — rather than a limited snapshot.
Standard deliverables include single-cell segmentation, marker quantification, and cell-phenotyping outputs. Our Research Analytics team can layer on additional spatial statistics, neighborhood analysis, and custom visualizations depending on your study's biological questions.
Timelines depend on panel size, number of tissue sections, and requested analysis depth, but multi-cycle staining and imaging generally take longer than single-marker IHC. Your scientific lead will provide a project-specific timeline once panel and cohort size are finalized.
Yes, panel design is a collaborative process. Our team can help select and validate antibodies suited to your biological question, tissue type, and existing literature, or work from a panel you already have in mind.
The representative multiplex immunofluorescence image featured on our services page shows a tertiary lymphoid structure in melanoma tissue, illustrating the kind of detailed immune architecture that CycIF and spatial biology approaches can reveal within the tumor microenvironment.
Advanced digital spatial profiling for translational research
Questions about region-of-interest protein and RNA profiling using the GeoMx Digital Spatial Profiler.
GeoMx DSP is a NanoString spatial biology platform that allows investigators to select specific regions of interest on a tissue section and profile them for protein or RNA expression, combining the spatial context of imaging with the quantitative depth of molecular profiling.
While CycIF and multiplex IHC provide single-cell resolution imaging of protein markers, GeoMx profiles user-defined regions of interest (which can be as small as individual cell segments) for larger protein or whole-transcriptome panels, offering broader molecular depth per region rather than pixel-level imaging across the entire panel.
Yes. GeoMx supports both protein panels (using antibody-based probes) and RNA panels (including whole-transcriptome atlas panels), and in some workflows both modalities can be assessed from serial sections of the same tissue block.
GeoMx DSP is most commonly run on FFPE tissue sections. Tissue quality and RNA/protein integrity affect data quality, so our team evaluates sample suitability during project scoping and can advise on optimal fixation and storage practices.
Regions of interest can be selected using morphology markers (such as tumor, immune, or stromal compartment stains) to guide segmentation, or defined manually based on pathologist annotation, allowing you to target specific tissue compartments relevant to your biological question.
It means GeoMx is particularly well suited to translational studies — such as clinical trial correlative work — where investigators want to understand how gene or protein expression varies across distinct tissue compartments (e.g., tumor core versus invasive margin) without losing spatial context.
GeoMx supports multi-slide runs, making it practical for cohort-level studies. Exact throughput depends on panel choice and the number of regions of interest per slide; our team can help plan a study design that balances cohort size, statistical power, and budget.
You'll receive region-level (and, where applicable, segment-level) expression data, along with quality-control metrics and normalized datasets ready for downstream statistical analysis. Our Research Analytics team can also provide custom visualizations and differential expression analysis.
Yes, this is a common and powerful study design. Because GeoMx generates region-specific molecular data, it pairs well with single-cell resolution imaging from CycIF or with bulk sequencing data, allowing multi-layered interpretation of the same tissue.
Yes — our team is happy to walk through the GeoMx workflow, panel options, and example data during an initial consultation so you can determine whether it's the right fit for your research question before finalizing a project plan.
Certified Olink® Service Provider
Questions about proximity extension assay (PEA) proteomics for blood and biofluid biomarker profiling.
Olink is a high-throughput proximity extension assay (PEA) platform for multiplex protein biomarker profiling in blood and other biofluids. As a Certified Olink Service Provider, IMCO has met Olink's standards for instrumentation, technical training, and quality control, giving you confidence in the reliability of results generated in our lab.
In PEA, two antibodies labeled with unique DNA oligonucleotides bind simultaneously to a target protein. When in close proximity, the oligos hybridize and are extended by a DNA polymerase, generating a unique DNA barcode for that protein, which is then amplified and read out by qPCR or next-generation sequencing.
Olink panels are validated primarily for serum, plasma, and other biofluids, though some panels can accommodate additional matrices. Our team can advise on minimum volume requirements and collection/storage best practices for your specific sample type.
Olink panels range from smaller, focused panels covering specific biological pathways to larger, high-throughput panels measuring thousands of proteins simultaneously. Panel selection depends on your research question, and our team can help identify the panel(s) best aligned with your study.
Olink data can be read out using either qPCR-based platforms or next-generation sequencing (NGS), depending on the specific panel and study needs. Your scientific lead will discuss which readout is most appropriate for your project during scoping.
Olink's PEA chemistry is designed to work with very small sample volumes, which makes it well suited to precious or limited biospecimens such as pediatric samples or serial longitudinal collections. Exact volume requirements depend on the panel(s) selected.
Yes. Olink protein data is frequently paired with transcriptomic data (such as RNA-seq) or with spatial tissue data to build a more complete picture connecting circulating biomarkers with tissue-level biology.
As a certified service provider, we follow Olink's standardized QC protocols, including internal and external controls on every plate, to flag and address assay variability before data are released, helping ensure that results are reliable and comparable across runs.
Olink data are typically reported as Normalized Protein Expression (NPX) values, an arbitrary log2 scale optimized for relative comparisons between samples. Our team provides normalized datasets along with QC reports and can support downstream statistical analysis of NPX data.
Yes, Olink's high sample throughput and low volume requirements make it well suited to longitudinal sampling and large cohort studies, including clinical trial correlative work where tracking biomarker changes over time is a key objective.
Multiple markers, one tissue section
Questions about multiplex immunohistochemistry panels, scoring, and tissue-sparing staining strategies.
Multiplex IHC allows several protein markers to be visualized simultaneously on a single tissue section using distinct chromogens or fluorophores, rather than requiring a separate slide and stain for each marker. This preserves tissue and lets you assess co-localization and spatial relationships between markers directly.
Panel size depends on the detection chemistry and tissue characteristics, but our multiplex IHC workflow is designed to accommodate multiple markers per slide, offering a middle ground between single-marker IHC and the highest-plex spatial platforms like CycIF.
It means you can conserve limited or precious tissue by staining several markers of interest on a single section rather than using separate sections for each marker, which is especially valuable for small biopsies or archival specimens with limited material.
Multiplex IHC is most commonly performed on FFPE tissue sections, similar to standard IHC. Our team can advise on section thickness, fixation, and other pre-analytical factors that affect staining quality.
Both options are available. We can run established, validated multiplex panels for common applications (such as immune checkpoint or lymphocyte subset panels), or work with you to design and validate a custom panel tailored to your specific research question.
Deep immunophenotyping, dozens of parameters
Questions about high-parameter mass cytometry for comprehensive single-cell immune profiling.
CyTOF (mass cytometry) uses metal-tagged antibodies and time-of-flight mass spectrometry instead of fluorophores and lasers, largely eliminating spectral overlap. This allows dozens of parameters to be measured simultaneously on single cells, far exceeding what is practical with conventional fluorescence-based flow cytometry.
CyTOF panels can include dozens of markers per cell in a single tube, enabling deep immunophenotyping of complex cell populations without the need for multiple parallel panels, which is a major advantage for characterizing rare or heterogeneous cell subsets.
CyTOF is typically performed on live or fixed single-cell suspensions, including PBMCs, dissociated tissue, and whole blood preparations. Sample viability and cell count requirements will be discussed during project scoping to ensure a successful run.
Deep immunophenotyping refers to comprehensively characterizing immune cell populations — including rare subsets, activation states, and functional markers — in a single experiment. This level of detail is particularly valuable for understanding complex immune responses in cancer, autoimmunity, and infectious disease research.
Both are available. We offer established panels for common immunophenotyping applications, and our team can also help design and validate a custom metal-conjugated antibody panel tailored to the cell populations and markers most relevant to your study.
From mutational landscape to functional biology
Questions about WES and RNA-Seq, including sample requirements, bioinformatics, and turnaround.
We offer Whole Exome Sequencing (WES) for characterizing the mutational landscape of tumor and normal tissue, and RNA-Seq for profiling gene expression and functional biology, allowing investigators to connect genomic alterations with their downstream transcriptional consequences.
WES captures the protein-coding regions of the genome to identify mutations, copy number alterations, and other DNA-level changes, while RNA-Seq measures gene expression and can reveal pathway activity, immune infiltration signatures, and fusion transcripts. Many studies benefit from pairing both to link genotype with functional phenotype.
Both FFPE and fresh-frozen tissue can be used, along with extracted DNA or RNA if you already have nucleic acids prepared. FFPE material can be more challenging for RNA integrity, so our team will assess sample quality and recommend the best approach during scoping.
A matched normal sample (such as adjacent normal tissue or blood) is recommended for WES to reliably distinguish somatic mutations from germline variants, though tumor-only sequencing with appropriate bioinformatic filtering is also possible depending on your study goals.
Sequencing depth is tailored to your study objectives — for example, higher depth may be needed to detect low-frequency subclonal mutations in WES, or to capture lowly expressed transcripts in RNA-Seq. Your scientific lead will recommend appropriate depth based on your research question and sample type.
The foundation every downstream assay relies on
Questions about tissue embedding, sectioning, H&E staining, TMA construction, and pathologist review.
The Histopathology Shared Resource handles the foundational tissue-processing steps that every downstream assay relies on — including tissue embedding, sectioning, standard H&E staining, and slide preparation — ensuring high-quality starting material for all of our specialized assays.
Because the quality of tissue processing directly affects the success of every downstream technique — from IHC and CycIF to sequencing — poor sectioning, fixation, or staining can compromise results regardless of how advanced the downstream assay is. Starting with expertly prepared tissue is essential.
The team routinely processes FFPE tissue blocks as well as fresh and frozen tissue, handling embedding, sectioning, and slide preparation for a wide range of tissue types and study designs.
In addition to standard H&E, the resource can support specialized histochemical stains, tissue microarray (TMA) construction, and slide preparation tailored to the requirements of downstream assays such as IHC, multiplex imaging, or nucleic acid extraction.
Yes, pathologist review and annotation — such as identifying regions of interest, confirming tumor content, or assessing tissue quality — can be incorporated into a project, which is particularly useful for guiding downstream assays like GeoMx region selection.