einarolafsson/spacr-example-measure

spaCR — Measure example data

Example input for the Measure module of spaCR. These are the merged arrays a Mask run produces, so Measure can be run end to end without first segmenting anything.

What is here

Path	What it is
merged/*.npz	16 fields, compressed. Each holds one array under the key image.
measurements.db	The Mask run's object counts (object_counts, pivoted_counts, run_status).
settings/	The exact settings the Mask run used, as CSV and JSON.
qc/	Per-object segmentation QC tables from that run.

The arrays

Each field is (1994, 1994, 7) uint16, channels last:

Channel	Contents
0–3	Image channels, as acquired
4	Cell label mask
5	Nucleus label mask
6	Pathogen label mask

Channels 4–6 are label images — each object is a distinct integer, 0 is background — not binary masks.

Plate layout

Four wells, four fields each, taken from a 13-field-per-well plate:

E01   fields 1, 9, 10, 11
E02   fields 1, 9, 10, 11
L01   fields 1, 9, 10, 11
L02   fields 1, 9, 10, 11

The four wells are kept deliberately: dropping to a single well would make well-level aggregation and between-condition comparison untestable, which is most of what Measure does after the per-object step.

Using it

spaCR downloads this on first use from the Measure module. To use it directly:

import numpy as np
from huggingface_hub import snapshot_download

path = snapshot_download("einarolafsson/spacr-example-measure",
                         repo_type="dataset")
field = np.load(f"{path}/merged/plate1_E01_1_1.npz")["image"]
cell_labels = field[..., 4]

The .npz compression is a transport detail — it halves the download and is decompressed on load. Measure reads .npy, so spaCR's own downloader writes them out as .npy once, on arrival.

How spaCR downloads it

Everything here is also published as a single uncompressed spacr-example-measure.tar, and that is what spaCR fetches: one request instead of 23, a progress figure that means something, and a download that stops when you press Cancel. It is unpacked with tar's data filter, which refuses any member that would write outside the destination folder.

The individual files are kept beside it so the set can be browsed and previewed on this page. They are the same bytes; either is fine to use.

Provenance

Produced by spaCR's Mask module (preprocess_generate_masks) from spaCR's own example images, with cpsam for cells and nuclei and a Toxoplasma-specific CPSAM checkpoint for pathogens. The settings that produced it are in settings/; absolute paths in them have been replaced with placeholders.