Sold by: Biohub
Open data
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Deployed on AWS
DynaCell is an evaluation framework for dynamic 3D virtual staining of live cells.
The dataset pairs label-free transmitted-light volumes (phase reconstructions from brightfield z-stacks) with fluorescence ground truth for four organelles (nucleus, cell membrane,
endoplasmic reticulum, mitochondria) across three conditions
(uninfected, Zika-infected, Dengue-infected).
The v1 release contains images of A549 human lung adenocarcinoma cells acquired on
the Mantis correlative label-free and light-sheet fluorescence microscope at Biohub
(24 OZX stores, 262 FOVs, ~407 GB), split into train and test sets across 4 organelle
markers and 3 conditions.
A v1.1 release will add the WTC-11 hiPSC component: cells from the Allen Institute
hiPSC single-cell image dataset (Viana et al., Nature 2023), reprocessed as paired
label-free and confocal fluorescence volumes. The iPSC dataset is redistributed under
the Allen Institute Terms of Use (https://www.allencell.org/terms-of-use.html), which
requi[...]
Overview
DynaCell is an evaluation framework for dynamic 3D virtual staining of live cells. The dataset pairs label-free transmitted-light volumes (phase reconstructions from brightfield z-stacks) with fluorescence ground truth for four organelles (nucleus, cell membrane, endoplasmic reticulum, mitochondria) across three conditions (uninfected, Zika-infected, Dengue-infected).
The v1 release contains images of A549 human lung adenocarcinoma cells acquired on the Mantis correlative label-free and light-sheet fluorescence microscope at Biohub (24 OZX stores, 262 FOVs, ~407 GB), split into train and test sets across 4 organelle markers and 3 conditions.
A v1.1 release will add the WTC-11 hiPSC component: cells from the Allen Institute hiPSC single-cell image dataset (Viana et al., Nature 2023), reprocessed as paired label-free and confocal fluorescence volumes. The iPSC dataset is redistributed under the Allen Institute Terms of Use (https://www.allencell.org/terms-of-use.html ), which requires citation of the original dataset and limits use to noncommercial research.
All data are stored as RFC-9 zipped OME-Zarr (.ozx) archives following OME-NGFF v0.5, readable with iohub (https://github.com/czbiohub-sf/iohub ). Machine-readable metadata (Croissant JSON-LD with Responsible AI fields, per the NeurIPS Datasets & Benchmarks track) is published at s3://dynacell/v1/metadata/croissant.json.
Features and programs
Open Data Sponsorship Program
This dataset is part of the Open Data Sponsorship Program, an AWS program that covers the cost of storage for publicly available high-value cloud-optimized datasets.
Pricing
This is a publicly available data set. No subscription is required.
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AWS Data Exchange (ADX)
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Open data resources
Available with or without an AWS account.
- How to use
- To access these resources, reference the Amazon Resource Name (ARN) using the AWS Command Line Interface (CLI). Learn more
- Description
- DynaCell v1 release: paired label-free and fluorescence 3D+time volumes in RFC-9 zipped OME-Zarr (.ozx) format. Contains biohub-a549 (train/test splits, 4 markers x 3 conditions = 24 stores), Croissant 1.1 metadata with Responsible AI fields, and placeholders for forthcoming demo samples, trained model checkpoints, and supplementary movies.
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::dynacell
- AWS region
- us-west-2
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://dynacell/
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How to cite
DynaCell was accessed on DATE from https://registry.opendata.aws/dynacell .