Proposed Enhancements to caMicroscope: AI-Powered Tissue Analysis and Spatial Transcriptomics Integration

[Prachethan7]

Hi @birm @tdiprima ,

I’d like to propose a few ideas to enhance caMicroscope by integrating AI, pathology, and spatial transcriptomics. These features aim to improve the platform’s capabilities for researchers and pathologists working with whole slide images (WSIs) and spatial data. I’m enthusiastic about contributing to these ideas and am eager to collaborate with the community to bring them to fruition.

Proposed Improvements

1. Classifying Tissue Regions in Whole Slide Images (WSIs)

• Feature Addition: Develop an AI-powered module to automatically classify regions within WSIs, such as tumor, stromal, and immune regions.
• Platform Integration: Overlay classification results on WSIs for better visualization and diagnosis.
• User Interaction: Include tools for exporting classified regions and customizing threshold parameters.

2. Mapping Spatial Relationships in Tumor Microenvironment

• Feature Addition: Introduce tools to map spatial relationships between tumor cells, immune cells, and stromal cells.
• Improvements: Visualize proximity and interaction patterns using scatterplots, heatmaps, and spatial annotations.
• Research Application: Enable users to study immune infiltration, tumor microenvironment structure, and progression mechanisms.

3. Gene Expression and Tumor Progression Analysis

• Feature Addition: Integrate spatial transcriptomics data with WSIs, providing overlays of gene expression heatmaps directly on tissue slides.
• Improvements: Offer tools to correlate gene expression patterns with histological features to study tumor progression and metastasis.
• User Benefit: Facilitate exploration of how gene expression drives tumor development in context with tissue morphology.

4. Visualization of Spatial Transcriptomics Data

• Feature Addition: Develop interactive visualizations for spatial transcriptomics datasets, including:
  • Zoomable tissue maps showing gene expression data.
  • Linked dimensionality reduction plots (e.g., UMAP, t-SNE) to visualize gene clusters.
• User Interaction: Allow users to query specific genes and visualize their spatial distributions dynamically.

Feedback and Suggestions
I would love your input on the following:

1. Do these ideas align with caMicroscope’s goals and current feature set?
2. Are there specific datasets or existing modules that I could build upon for these improvements?
3. What additional functionalities or visualization options would be most helpful for the caMicroscope community?

I’m passionate about making these ideas a reality and would be thrilled to contribute to caMicroscope. Looking forward to your thoughts and suggestions!