HiTIF works with CCR collaborators to evaluate project feasibility, define the appropriate imaging or bioinformatics workflow, clarify collaboration expectations, and connect projects with available development, analysis, and subsidy resources.
Consultation
The investigator contacts the Facility Head to discuss the availability of instrumentation and personnel and to evaluate the feasibility of the proposed project on both biological and technological grounds.
Key considerations include the choice of fluorophores, whether the phenotype of interest can be detected by confocal microscopy and is suitable for High-Content Imaging (HCI), the availability of appropriate positive and negative controls, and the size of the assay window.
Preliminary low-throughput results, ideally including fluorescence microscopy data, are essential to assess whether the assay can be miniaturized to a high-throughput format. During these discussions the HiTIF advises on assay design and determines which of its four platforms best fits the project.
Collaboration and Authorship
Most HiTIF projects run as collaborations, with the lead contact trained on the relevant instrumentation, wet-lab protocols, and/or analysis pipelines.
Given the technical resources and intellectual contributions the HiTIF provides, we expect authorship on resulting publications; alternatively, the HiTIF offers training and instrument/software access as a service, with acknowledgement.
Projects are selected on technical feasibility and handled on a first-come, first-served basis, except manuscripts in revision. Demand that exceeds capacity is handled through a formal Oversight Committee evaluation.
Platform
Arrayed High-Content Imaging (HCI)
Arrayed HCI is suited to assays that can be miniaturized to 96- or 384-well format, are compatible with liquid automation, and can draw on an off-the-shelf oligo RNA library.
The HiTIF optimizes growth conditions, image acquisition, and siRNA/sgRNA transfection, and designs custom image analysis pipelines with quality-control descriptors such as Z-score, S/N ratio, and assay window to guide optimization.
A pilot screen validates the workflow before primary screening in multiple replicates, and selected hits undergo secondary screening to rule out off-target effects.
Platform
Pooled HCI
Pooled HCI is used when an arrayed off-the-shelf library is not available and/or when a custom library is needed for functional genomic screens.
In this case, the HCI phenotypic readout needs to be compatible with in situ sequencing (ISS). The lead contact is trained on the full wet-lab protocol and runs the experiment with HiTIF assistance.
The HiTIF performs the downstream Imaging Bioinformatics analysis that links single-cell phenotypes to guide identity.
Platform
Imaging Bioinformatics (IB)
For projects that use externally generated images, the HiTIF assesses whether the datasets are suited to HCI analysis with its open-source pipelines.
Execution is carried out primarily by the HiTIF, or shared with the collaborator trained on selected pipeline steps, depending on analysis complexity.
Platform
Spatial Bioinformatics (SB)
The HiTIF does not generate spatial omics data in house. Collaborators first engage the CCR Single Cell Sequencing Core (SCSC) or the Spatial Imaging and Transcriptomics Resource (SpITR) for data generation.
After data generation, the HiTIF takes over the downstream spatial analysis.
STARS Subsidy for HiTIF Projects
To help offset project-based costs, HiTIF collaborators have access to two external cost-sharing mechanisms offered through the CCR Office of Science and Technology Resources (OSTR). OSTR provides up to 50% of the total project cost, to a maximum of $8,000 per PI per fiscal year. For projects above this threshold, PIs can submit requests via the CCR Supplemental Technology Award Review System (STARS), which can cover up to $30,000 of incurred cost. Larger STARS applications require an experimental plan and scientific and budgetary justification and are reviewed by a panel of HiTIF-independent experts. As with all such applications, subsidies should be requested before work begins.
For more information and/or questions about the STARS subsidies for HiTIF projects please contact Mariam Malik or Gianluca Pegoraro.