Example datasets#

Piximi includes several example datasets. They are described below along with their sources and licenses. If you use any of the example datasets in a publication, please also cite the original dataset with the citation provided below.

MNIST#

mnistExampleIcon

MNIST (Modified National Institute of Standards and Technology) is a database of handwritten digits often used in machine learning. Images are grayscale and 28x28 pixels and each image contains a single digit. We provide a small subset of the full MNIST database.

We accesesd MNIST from a website provided by the original authors.
MNIST licencse: CC-BY-SA-3
MNIST citation doi: 10.1109/5.726791

C. elegans#

cElegansExampleIcon

Caenorhabditis elegans is a nematode worm and is a commonly used model organism. This dataset is images of transgenic C. elegans expressing the promoter of gene clec-60 fused to GFP (clec-60:GFP) and an mCherry pharynx label. In wild type worms, clec-60:GFP is expressed in posterior intestinal cells while in pmk-1(km25) mutants the clec-60:GFP is elevated in expression and visible in the anterior intestine, close to the pharynx. There are multiple worms visible in each image. Channel 1 is GFP, channel 2 is mCherry.

The C. elegans data were provided by Javier Irazoqui as BBBC012 in the Broad Bioimage Benchmark Collection.
C. elegans license: CC0
C. elegans citation doi: 10.1038/nmeth.2083

Human U2OS-cells#

humanU2OSCellsExampleIcon

These human U2OS cells express b-arrestin-GFP and an orphan GPCR. When the GPCR is stimulated, b-arrestin-GFP is recruited to the plasma membrane and eventually endocytosed resulting in vesicle like structures. Channel 1 is GFP, channel 2 is DNA.

The U2OS cells data were provided by Ilya Ravkin as BBBC016 in the Broad Bioimage Benchmark Collection.
U2OS licence: CC-BY-3
U2OS citation doi: 10.1038/nmeth.2083

Human U20S-cells cytoplasm crops#

BBBC013ExampleIcon

These human U2OS osteosarcoma cells are stably transfected with fluorescently tagged Forkhead protein (FKHR-EGFP). In proliferating cells, FKHR-EGFP is constantly trafficking between nucleus and cytoplasm. When treated with drugs that prevent PI3 kinase/PKB signaling, nuclear export is inhibited and FKHR-EGFP accumulates in the nucleus. Channel 1 is FKHR-GFP, channel 2 is DNA.

The U2OS cells cytoplasm crop data were provided by Ilya Ravkin as BBBC013 in the Broad Bioimage Benchmark Collection.
U2OS licence: CC-BY-3
U2OS citation doi: 10.1038/nmeth.2083

Human PLP1 localization#

PLP1ExampleIcon

These human HeLa cells express either wild type or the disease-associated variant of PLP1 protein, which localizes differently than the healthy version.
Channel 1 is artifacts, channel 2 is fluorescently tagged protein PLP1, and channel 3 is DNA.

The human PLP1 localization data were provided by Jessica Lacoste in Mikko Taipale’s lab at University of Toronto.
Human PLP1 licence: CC0
Human PLP1 citation doi: 10.1016/j.cell.2024.09.003