spacr
Datasets
All datasets matching “spacr”spacr_settingsspacr-example-annotate
spaCR — Annotate and Classify example data
Example input for the Annotate and Classify modules of
spaCR. It is the output of a Measure
run, so both modules can be exercised without segmenting or measuring anything
first.
What is here
Path
What it is
data/
2,341 single-cell PNG crops, foldered by phenotype
measurements.db
The measurements, plus png_list and the annotation tables
measurements/active_learning/
The model card from the first annotation… See the full description on the dataset page: https://huggingface.co/datasets/einarolafsson/spacr-example-annotate.spacr-tutorials
spaCR tutorial media
Narration and 4K video for the spaCR
interactive tutorial library, served directly to
https://einarolafsson.github.io/spacr/tutorials/.
spaCR is a toolkit for microscopy and single-cell analysis of pooled CRISPR
screens. This repository holds the media its 40-lesson tutorial player streams;
it is not a training dataset.
Why it lives here
GitHub Pages caps a published site at 1 GB. The full narration set is 2,662 MiB
across 54 voices, so the… See the full description on the dataset page: https://huggingface.co/datasets/einarolafsson/spacr-tutorials.spacr-example-make-masks
spaCR — Make Masks test data
Ten fluorescence microscopy fields of Toxoplasma gondii parasitophorous
vacuoles, each with a curated instance mask. This is the data behind the
Load test data… button on the Make Masks screen of
spaCR.
Where the images come from
All ten are the lab's own acquisitions. They come from the in-house part
(toxoplasma_pv) of spaCR's Toxoplasma vacuole training set, and each one's
row in that set's manifest is reproduced below and in… See the full description on the dataset page: https://huggingface.co/datasets/einarolafsson/spacr-example-make-masks.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… See the full description on the dataset page: https://huggingface.co/datasets/einarolafsson/spacr-example-measure.spacr-example-screen