FishFeats

FishFeats streamlines extraction of quantitative single-cell data from multimodal 3D fluorescent microscopy images, including smFISH expression, immunohistochemical staining, cell morphologies, and cell classification, into a unified cell-by-cell table for downstream analysis.

Key Features:

• Integrated image analysis pipeline: Combines segmentation of cells and nuclei, detection of RNA transcripts or other staining, and assignment of nuclei and RNA dots to their corresponding cell within a single framework.
• Multimodal data extraction: Extracts smFISH expression in individual cells, immunohistochemical staining, cell morphologies, and cell classification from 3D fluorescent microscopy images.
• Manual correction capability: Enables manual correction of each analysis step to address measurement sensitivity to small errors in automated processing.

Scientific Applications:

• Single-cell spatial transcriptomics: Quantifies smFISH expression at single-cell resolution in intact 3D tissues.
• Multimodal tissue imaging analysis: Integrates nuclear segmentation, cell segmentation, RNA transcript detection, and protein staining data for comprehensive cell-by-cell profiling.
• Cell morphology and classification: Extracts cellular morphological parameters and classification labels alongside molecular measurements.

Methodology:

FishFeats is implemented as a Napari plugin in Python, leveraging available efficient software applications for image analysis steps including segmentation, transcript detection, and multimodal data integration.