FInCH

FInCH automates whole-image analysis of protein expression and cell morphology in immunohistochemistry slides, enabling simultaneous assessment of cellular processes and their effects at the tissue scale with positional information for longitudinal analyses.

Key Features:

• Multi-scale data collection: Collects data at customizable scale from the cell-level to the entire structure.
• Positional information recording: Records each data point with positional information to account for ontogenetic transformation of structures and variation in slide positioning.
• Scalable grid system: Uses a scalable grid to account for ontogenetic transformation of structures and variation in slide positioning.
• Customizable file manager: Outputs collected data in association with full details of image classification including ontogenetic stage, population, and IHC assay.
• Multi-transcription factor analysis: Measures expression of multiple transcription factors simultaneously.

Scientific Applications:

• Developmental biology: Automated measurement of morphology and expression of eight transcription factors across 12 developmental stages in beak tissues of a wild passerine bird.
• Longitudinal morphogenesis studies: Analysis of growing structures that change size and shape over developmental time with preserved positional information for alignment.
• Population-level comparative analysis: Recording of more than six million cells with full positional information across 25 study populations.
• Immunohistochemistry analysis: Applicable to IHC slides from any imaging platforms and transcriptional factors.

Methodology:

FInCH is implemented as a python-based application and distributed as an open-source Fiji plugin.