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.

Metadata

Release files for jump-portrait 0.1.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for jump-portrait 0.1.1
File	Size	Uploaded
jump_portrait-0.1.1.tar.gz	10.1 kB	Apr 14, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for jump-portrait 0.1.1
File	Interpreter	ABI	Platform	Reset
jump_portrait-0.1.1-py3-none-any.whl 12.3 kB Apr 14, 2026	Python 3	none	any	Details

Total release size: 22.4 kB

Release files / jump_portrait-0.1.1.tar.gz

Download URL	jump_portrait-0.1.1.tar.gz
Size	10.1 kB
Tags	Source
SHA-256 checksum How to use checksums	`0ce6e0ab936752e3e27ac8c4d9bbd5309bfe405a003b30a1addeb0ba3a62a6a4`
BLAKE2b-256 checksum How to use checksums	`6ed4de3f5cee24afa67dbed354988246a14ca00511df1aa6d023735e3c015274`
Upload date	Apr 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.11.2 {"installer":{"name":"uv","version":"0.11.2","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"NixOS","version":"26.05","id":"yarara","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}`

Release files / jump_portrait-0.1.1-py3-none-any.whl

Download URL	jump_portrait-0.1.1-py3-none-any.whl
Size	12.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`6a2883b973220ea0ed6a562c01224ab73f3539d7c3e03eeca7943442551fe303`
BLAKE2b-256 checksum How to use checksums	`18ab6d868adb9acba4c5b6e0c5daaadcb3877ed957e823c5010cf2460d9852c9`
Upload date	Apr 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.11.2 {"installer":{"name":"uv","version":"0.11.2","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"NixOS","version":"26.05","id":"yarara","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}`