Cellpainting Tools

Configuration File: cellpainting_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the cellpainting_tools.json configuration file.

Available Tools

CellPainting_get_screen_plates (Type: CellPaintingTool)

Get the list of plates in a Cell Painting screen from the Image Data Resource (IDR). Returns plat…

CellPainting_get_screen_plates tool specification

Tool Information:

  • Name: CellPainting_get_screen_plates

  • Type: CellPaintingTool

  • Description: Get the list of plates in a Cell Painting screen from the Image Data Resource (IDR). Returns plate IDs and names for the given screen. Use CellPainting_search_screens first to find valid screen IDs. Example: Get all plates in idr0016 screenA (screen_id=1251).

Parameters:

  • operation (string) (required) Operation type

  • screen_id (integer) (required) IDR screen identifier (e.g., 1251 for idr0016 screenA)

Example Usage:

query = {
    "name": "CellPainting_get_screen_plates",
    "arguments": {
        "operation": "example_value",
        "screen_id": 10
    }
}
result = tu.run(query)

CellPainting_get_well_data (Type: CellPaintingTool)

Get well-level metadata and image links for a specific plate in a Cell Painting experiment from t…

CellPainting_get_well_data tool specification

Tool Information:

  • Name: CellPainting_get_well_data

  • Type: CellPaintingTool

  • Description: Get well-level metadata and image links for a specific plate in a Cell Painting experiment from the Image Data Resource (IDR). Returns well IDs, row/column positions, well URLs, and links to microscopy images. Use CellPainting_get_screen_plates to find valid plate IDs. Example: Get the first 5 wells of plate 5104 from idr0016.

Parameters:

  • operation (string) (required) Operation type

  • plate_id (integer) (required) IDR plate identifier (e.g., 5104 for a plate in idr0016 screenA)

  • limit (integer) (optional) Maximum number of wells to return (default 20)

Example Usage:

query = {
    "name": "CellPainting_get_well_data",
    "arguments": {
        "operation": "example_value",
        "plate_id": 10
    }
}
result = tu.run(query)

CellPainting_search_screens (Type: CellPaintingTool)

List available Cell Painting screens/studies in the Image Data Resource (IDR). Returns screen nam…

CellPainting_search_screens tool specification

Tool Information:

  • Name: CellPainting_search_screens

  • Type: CellPaintingTool

  • Description: List available Cell Painting screens/studies in the Image Data Resource (IDR). Returns screen names, IDs, descriptions, and URLs. Automatically filters to Cell Painting and morphological profiling studies (e.g. idr0016 Wawer ~30,000 compounds, JUMP-CP). Use the optional query parameter to further filter by keyword. Example: Discover which Cell Painting datasets are available in IDR.

Parameters:

  • operation (string) (required) Operation type

  • query ([‘string’, ‘null’]) (optional) Optional keyword to filter screens by name or description (e.g., ‘JUMP’, ‘U2OS’, ‘wawer’)

Example Usage:

query = {
    "name": "CellPainting_search_screens",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)