jump-portrait 0.1.0

Tools to fetch and visualize JUMP images

JUMP-portrait

Utilities for interacting with the JUMP-Cell Painting Gallery dataset on AWS S3. We facilitate querying the JUMP-CP dataset index, retrieving metadata for specific perturbations, and loading microscopy images directly into memory or downloading them to local storage.

Main Functions

Metadata Retrieval

get_item_location_metadata

Search for a specific gene or compound by name or JCP ID to retrieve its location metadata (Source, Batch, Plate, Well, Site) and corresponding S3 URIs.

from jump_portrait.fetch import get_item_location_metadata

# Search for a gene by standard key
metadata = get_item_location_metadata("MYT1")

# Search for a compound by JCP ID
metadata = get_item_location_metadata("JCP2022_000001", input_column="JCP2022")

Image Retrieval

get_jump_image

Fetch a single image directly as a NumPy array using specific coordinate identifiers.

from jump_portrait.fetch import get_jump_image

img = get_jump_image(
    source="source_4",
    batch="2021_04_26_Batch1",
    plate="BR00121565",
    well="A01",
    channel="DNA",
    site=1
)

get_jump_image_batch

Load multiple images into memory in parallel based on a metadata table.

from jump_portrait.fetch import get_item_location_metadata, get_jump_image_batch

# Get metadata for a perturbation
metadata = get_item_location_metadata("MYT1")

# Load all DNA and Mito images for this perturbation into memory
meta_dicts, images = get_jump_image_batch(
    metadata, 
    channels=["DNA", "Mito"],
    site=[1, 2]
)

File Operations

download_jump_image_batch

Download a batch of images from S3 to a local directory in a structured or flattened format.

from jump_portrait.fetch import get_item_location_metadata, download_jump_image_batch

metadata = get_item_location_metadata("CLETVKMYAXARPO-UHFFFAOYSA-N")

# Download images to a local folder
download_jump_image_batch(
    metadata, 
    output_dir="./data/images", 
    channels=["DNA", "RNA"]
)

S3 Utilities

The jump_portrait.s3 module provides lower-level utilities for interacting with the Cell Painting Gallery:

• get_image_from_s3uri(uri): Retrieves an image from a specific S3 URI and returns it as a NumPy array. Supports .tif, .tiff, .png, and .npy formats.
• s3client(use_credentials=False): Creates a boto3 client configured for the gallery. By default, it uses unsigned requests (no AWS account required for public data).
• download_s3uri(meta, output_dir): Downloads a specific file from the gallery based on metadata components.