Microscopy Image Analysis

Deep learning microscopy pipelines that extract predictive insights from cellular images for biopharma R&D.

From Imaging to Quantitative Cellular Intelligence

Microscopy is now a high-dimensional data modality central to biopharma R&D. From whole-slide histopathology to high-content imaging, experiments generate rich datasets capturing morphological, spatial, and phenotypic signals – but translating them into reproducible, quantitative insights remains a bottleneck. Manual interpretation is subjective and unscalable, while traditional pipelines often miss biological complexity.

Aganitha addresses this by building deep learning–driven microscopy pipelines that convert raw images into structured, analyzable representations. Combining instance segmentation, multi-channel feature extraction, and phenotype modeling, these systems enable robust characterization of cell states, tissue architecture, and perturbation responses – shifting microscopy from descriptive imaging to predictive cellular intelligence for MoA studies, disease modeling, and therapeutic evaluation.

H&E stained WSI

Multi-gigapixel whole slide image analysis – nuclei segmentation, cell-type quantification, tumor grading, tissue classification, and morphological feature extraction using deep learning instance segmentation.

Immunofluroescence Images

High-content fluorescent imaging analysis – phenotypic fingerprinting across images, mechanism-of-action prediction, compound classification, and disease signature profiling from multi-channel morphological profiles.

Brightfield microscopy

Live-cell imaging analysis for organoid growth kinetics, toxicity screening, motility and tracking, and spheroid morphometry – with optional virtual H&E transformation from label-free images.

FISH image analysis

Fluorescence in situ hybridization analysis – gene amplification scoring (HER2/CEP17), chromosomal abnormality detection, RNA FISH expression quantification, and spatial transcriptomics.

Virtual staining

Aganitha uses deep learning to computationally convert unstained or label-free tissue images into virtually stained equivalents – H&E, IHC, PAS, Masson’s trichrome – without chemical processing. This enables multi-stain availability from a single biopsy and accelerates toxicity and formulation screening.

What Aganitha delivers

  • H&E Stained WSI Analysis: End-to-end computational pathology pipelines for cell-type detection, tissue classification, biomarker extraction, and tumor grading/classification.
  • Cell Painting Image Analysis: High-content analysis workflows for phenotypic profiling, enabling MoA prediction, disease signature identification, and compound classification.
  • Brightfield Microscopy Image Analysis: Label-free imaging analytics for growth kinetics, toxicity screening, and cell motility/tracking, with virtual staining to extend H&E/cell painting outcomes.
  • FISH Image Analysis: Quantitative spatial imaging pipelines for gene amplification detection, chromosomal abnormalities, and spatial gene expression mapping.
  • Virtual Staining: AI-based transformation of unstained or single-stain images into multi-stain outputs (H&E, PAS, IHC, fluorescent), enabling cost-efficient workflows and enhanced downstream analysis.
Why Aganitha

The Aganitha Advantage

Biology-First AI

Our models are designed with domain expertise, trained and validated by scientists who understand the biological context, not just the pixel statistics.

2D to 3D Native

Native support for 2D and 3D imaging modalities, including organoid and tissue section analysis.

Label-Free Intelligence

Brightfield and virtual staining pipelines reduce dependency on expensive fluorescent protocols while preserving analytical richness across phenotypic endpoints.

Multi-Modal Ready

Engineered for integration with genomics, transcriptomics, and proteomics, delivering a unified view of biological state that imaging alone cannot provide.

Discover our offerings across the biopharma value chain

Our Solutions

Customizable platforms and solutions across the drug discovery value chain from target discovery to therapeutic development
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Our Services

Offering services in computational sciences and technology to complement biopharma R&D
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Case Studies

Helping clients accelerate drug discovery and development by building computational biology, computational chemistry, technology, and cloud solutions
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Talk to our imaging AI team about your specific cell biology or discovery challenge.

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