deep-visual-proteomics-agent

Core Capabilities

1. AI Image Segmentation: Deep learning models segment cells and identify phenotypes from brightfield, H&E, or immunofluorescence images.

2. Phenotype Classification: CNN/transformer classifiers identify cell types, disease states, and morphological abnormalities.

3. LMD Coordinate Generation: Automated generation of laser microdissection coordinates for cells of interest.

4. MS Data Integration: Processes MaxQuant/DIA-NN output to link protein abundances to spatial coordinates.

5. Spatial Proteome Mapping: Creates spatially-resolved proteome maps linking morphology to molecular profiles.

6. Biologically-Informed Analysis: Neural networks incorporating pathway knowledge for interpretable biomarker discovery.

Example Usage

User: "Identify tumor vs. stroma cells in this H&E image and generate proteome profiles for each population."

Agent Action:

Key Components

Component	Tool/Method	Description
Segmentation	Cellpose, StarDist	Instance segmentation of cells
Classification	Custom CNN/ViT	Phenotype assignment
LMD Interface	Leica LMD7, PALM	Coordinate export formats
MS Processing	MaxQuant, DIA-NN	Protein quantification
Integration	Custom Python	Spatial mapping