Datasets

We maintain an API to let users access a handful of curated datasets for learning how to use starfish, and benchmarking algorithms and pipelines.

starfish.data.BaristaSeq(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads a BaristaSeq dataset generated from mouse visual cortex. The extracted field of view comes from an internal layer of V1 (range: 2-5). These data are published here:

https://doi.org/10.1093/nar/gkx1206

The data consist of 204 images acquired from 3 rounds, 4 channels, and 17 z-planes. Each image is (1000, 800) in (y, x)

Parameters
use_test_databool

Not used.

Returns
Experiment
Return type

Experiment

starfish.data.DARTFISH(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads an experiment with a single field of view from unpublished data generated with DARTFISH v1 2017, produced by imaging human occipital cortex. These data were donated by the Zhang lab as part of the SpaceTx consortium project.

The data consist of 18 images from 3 channels, 6 rounds, and 1 z-plane. Each image is (998, 998) in (y, x).

Parameters
use_test_databool

If True, returns a cropped Experiment where tiles are (170, 290) in (y, x)

Returns
Experiment
Return type

Experiment

starfish.data.ISS(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads an experiment containing a single field of view of In-Situ Sequencing data created by imaging human breast cancer tissue. The complete dataset is published:

https://doi.org/10.1038/nmeth.2563

The data consist of 16 images from 4 channels, 4 rounds, and a single z-plane. Each image is (1044, 1390) in (y, x)

Parameters
use_test_databool

If True, returns a cropped Experiment where images are (140, 200) in (y, x)

Returns
Experiment
Return type

Experiment

starfish.data.ImagingMassCytometry(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads an Imaging Mass Cytometry dataset donated to starfish by Denis Shapiro. This dataset consists of 52 fields of view.

Each field of view consists of 19 images acquired from 19 channels, 1 round, and 1 z-plane. Individual images have variable sizes, ranging from 400-500 pixels for each of (y, x).

Parameters
use_test_data:

Not used.

Returns
Experiment
Return type

Experiment

starfish.data.MERFISH(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads an experiment with a single field of view of MERFISH data derived from cultured U2-OS cells, published in the following manuscript:

https://doi.org/10.1073/pnas.1612826113

The data consist of 16 images from 8 rounds, 2 channels, and a single z-plane. Each image is (2048, 2048) (y, x)

Parameters
use_test_data: bool

If True, returns a cropped Experiment where tiles are (205, 405) (y, x)

Returns
Experiment
Return type

Experiment

starfish.data.MOUSE_V_HUMAN()[source]

Corresponds to sequencing 4 bases of the beta-actin gene in co-cultured mouse and human fibroblasts. These 4 bases only differ in one position, a SNP between species. as such, these data offer ground truth information to validate a cell typing exercise

https://www.ncbi.nlm.nih.gov/pubmed/23852452

Returns
Experiment
starfish.data.STARmap(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads a STARmap field of view generated from mouse primary visual cortex. These data are published:

https://doi.org/10.1126/science.aat5691

This dataset contains 696 images acquired across 6 rounds, 4 channels, and 29 z-planes. Each image is (1024, 1024) in (y, x)

Parameters
use_test_databool

Not used.

Returns
Experiment
Return type

Experiment

starfish.data.SeqFISH(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads a single field of view from a SeqFISH dataset generated from cultured mES cells. These data are published:

https://doi.org/10.1016/j.cell.2018.05.035

This dataset contains 1140 images acquired across 12 channels, 4 imaging rounds, and 29 z-planes. Each image is (2048, 2048) in (y, x)

Parameters
use_test_databool

If true, return a cropped Experiment where images are (280, 280) in (y, x)

Returns
Experiment
Return type

Experiment

starfish.data.allen_smFISH(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads an experiment with a single round from a single field of view of sequential smFISH data taken from mouse primary visual cortex. These data are unpublished, and were kindly contributed by the Allen Institute for Brain Science as a part of the SpaceTx consortium project.

The data consist of 102 images from 1 round, 3 channels, and 33 z-planes. Each image is (2048, 2048) (y, x). There are no test data.

Parameters
use_test_databool

Not used.

Returns
Experiment
Return type

Experiment

starfish.data.osmFISH(use_test_data:bool=False) → starfish.core.experiment.experiment.Experiment[source]

Loads an experiment containing 3 fields of view of osmFISH data generated by imaging mouse sematosensory cortex. The complete dataset is published:

https://doi.org/10.1038/s41592-018-0175-z

The data consist of 1755 images per field of view, taken over 13 rounds, 3 channels, and 45 z-planes. Each image is (2048, 2048) in (y, x)

Parameters
use_test_databool

If True, return a single round from one field of view, suitable for testing. The images are still (2048, 2048) in (y, x)

Returns
Experiment
Return type

Experiment