Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT.
Asa A BrockmanRohit KhuranaTodd BartkowiakPortia L ThomasShamilene SivagnanamCourtney B BettsLisa M CoussensChristine M LovlyJonathan Michael IrishRebecca A IhriePublished in: Cytometry. Part B, Clinical cytometry (2023)
Cyclic immunohistochemistry (cycIHC) uses sequential rounds of colorimetric immunostaining and imaging for quantitative mapping of location and number of cells of interest. Additionally, cycIHC benefits from the speed and simplicity of brightfield microscopy, making the collection of entire tissue sections and slides possible at a trivial cost compared to other high dimensional imaging modalities. However, large cycIHC datasets currently require an expert data scientist to concatenate separate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of proprietary software. Here, we present a unified and user-friendly pipeline for processing, aligning, and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and measures marker expression on each detected cell. Beyond straightforward single cell data analysis outputs, CASSATT explores the spatial relationships between cell populations. By calculating the log odds of interaction frequencies between cell populations within tissues and tissue regions, this pipeline helps users identify populations of cells that interact-or do not interact-at frequencies that are greater than those occurring by chance. It also identifies specific neighborhoods of cells based on the assortment of neighboring cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. CASSATT is a fully open source workflow tool developed to process cycIHC data and will allow greater utilization of this powerful staining technique.
Keyphrases
- single cell
- data analysis
- rna seq
- high resolution
- induced apoptosis
- electronic health record
- deep learning
- cell therapy
- high throughput
- cell cycle arrest
- gene expression
- stem cells
- cell death
- big data
- poor prognosis
- genome wide
- dna methylation
- physical activity
- optical coherence tomography
- endoplasmic reticulum stress
- single molecule
- bone marrow
- nitric oxide