Resources of the cell science accelerator at Allen Institute
Thank you for your interest in the open data, tools, and other free resources produced by the Allen Institute. To use our resources in your noncommercial research or for noncommercial purposes, you must cite them in accordance with our citation policy, which is available at alleninstitute.org/legal/citation-policy.
While we encourage you to use our resources for your noncommercial research or other noncommercial purposes, we want to ensure that our Content is afforded proper citation as detailed in the citation policy in all cases where it is used publicly. Your use of Content must be in compliant with our Terms of Use or agreed to in writing by the Allen Institute. For clarification about commercial use restrictions, please read the Terms of Use. If you are unsure about how to cite a source or would like written approval for a specific use that is otherwise prohibited, please send us a message.
Cell images
Dataset accessed through 3D Cell Viewer: the cell science accelerator at Allen Institute (2018). hiPSC Single-cell Image Dataset [dataset]. Available from allencell.org/3d-cell-viewer.
Datasets accessed through Cell Feature Explorer: the cell science accelerator at Allen Institute (year indicated on dataset). Name of dataset [dataset]. Available from cfe.allencell.org.
Dataset accessed through QUILT or bulk data download: the cell science accelerator at Allen Institute (2021). hiPSC Single-cell Image Dataset [dataset]. Available from allencell.org/data-downloading.
Drug perturbation pilot data
Dataset: the cell science accelerator at Allen Institute (2018). Drug perturbation pilot study [dataset]. Available from allencell.org/drug-perturbation-pilot.
Allen Integrated Cell – 3D Probabilistic Modeling and Label Free Determination
Code: the cell science accelerator at Allen Institute (2018). Allen Integrated Cell [software package]. Available from allencell.org/allen-integrated-cell.
Primary publication – label free: Ounkomol, C., Seshamani, S., Maleckar, M.M. et al. (2018). Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy. Nature Methods 15, 917–920. doi.org/10.1038/s41592-018-0111-2.
Allen Cell and Structure Segmenter
Code: the cell science accelerator at Allen Institute (2019). Allen Cell and Structure Segmenter [software package]. Available from allencell.org/segmenter.
AGAVE cell visualization tool
Code: the cell science accelerator at Allen Institute (2020). AGAVE 3D pathtrace image viewer [software package]. Available from allencell.org/pathtrace-rendering.
AICSImageIO
The cell science accelerator at Allen Institute (2021). AICSImageIO [software package]. Available from https://github.com/AllenCellModeling/aicsimageio.
FISH morphology code
The cell science accelerator at Allen Institute (2021). FISH Morphology Code [software package]. Available from https://github.com/AllenCellModeling/fish_morphology_code.
Primary publication: Gerbin, K.A. (2021). Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes. Cell Systems, 12(6), 670-687.E10. https://doi.org/10.1016/j.cels.2021.05.001.
Simularium
The cell science accelerator at Allen Institute (2021). Simularium Viewer: biological simulator and 3D visualization [software package]. Available from https://simularium.allencell.org.
While we encourage you to use our resources for your noncommercial research or other noncommercial purposes, we want to ensure that our Content is afforded proper citation as detailed in the citation policy in all cases where it is used publicly. Your use of Content must be in compliant with our Terms of Use or agreed to in writing by the Allen Institute. For clarification about commercial use restrictions, please read the Terms of Use. If you are unsure about how to cite a source or would like written approval for a specific use that is otherwise prohibited, please send us a message.
Cell images
Dataset accessed through 3D Cell Viewer: the cell science accelerator at Allen Institute (2018). hiPSC Single-cell Image Dataset [dataset]. Available from allencell.org/3d-cell-viewer.
Datasets accessed through Cell Feature Explorer: the cell science accelerator at Allen Institute (year indicated on dataset). Name of dataset [dataset]. Available from cfe.allencell.org.
Dataset accessed through QUILT or bulk data download: the cell science accelerator at Allen Institute (2021). hiPSC Single-cell Image Dataset [dataset]. Available from allencell.org/data-downloading.
Drug perturbation pilot data
Dataset: the cell science accelerator at Allen Institute (2018). Drug perturbation pilot study [dataset]. Available from allencell.org/drug-perturbation-pilot.
Allen Integrated Cell – 3D Probabilistic Modeling and Label Free Determination
Code: the cell science accelerator at Allen Institute (2018). Allen Integrated Cell [software package]. Available from allencell.org/allen-integrated-cell.
Primary publication – label free: Ounkomol, C., Seshamani, S., Maleckar, M.M. et al. (2018). Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy. Nature Methods 15, 917–920. doi.org/10.1038/s41592-018-0111-2.
Allen Cell and Structure Segmenter
Code: the cell science accelerator at Allen Institute (2019). Allen Cell and Structure Segmenter [software package]. Available from allencell.org/segmenter.
AGAVE cell visualization tool
Code: the cell science accelerator at Allen Institute (2020). AGAVE 3D pathtrace image viewer [software package]. Available from allencell.org/pathtrace-rendering.
AICSImageIO
The cell science accelerator at Allen Institute (2021). AICSImageIO [software package]. Available from https://github.com/AllenCellModeling/aicsimageio.
FISH morphology code
The cell science accelerator at Allen Institute (2021). FISH Morphology Code [software package]. Available from https://github.com/AllenCellModeling/fish_morphology_code.
Primary publication: Gerbin, K.A. (2021). Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes. Cell Systems, 12(6), 670-687.E10. https://doi.org/10.1016/j.cels.2021.05.001.
Simularium
The cell science accelerator at Allen Institute (2021). Simularium Viewer: biological simulator and 3D visualization [software package]. Available from https://simularium.allencell.org.
Lab resources
Cell lines
In text: [Name and number of cell line] developed at the cell science accelerator at Allen Institute (allencell.org/cell-catalog) and available through Coriell.
Primary publication: Roberts, B. et al. (2017). Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Molecular Biology of the Cell, 28(21). https://doi.org/10.1091/mbc.e17-03-0209.
Plasmids
In text: [Name and number of plasmid] developed at the cell science accelerator at Allen Institute (allencell.org/cell-catalog) and available through AddGene.
In acknowledgements: Acknowledge the cell science accelerator at Allen Institute for developing plasmid(s) used in the work.
Follow this formula for additional lab resources, including those provided to you directly by collaborators at the Allen Institute.
In text: [Name and number of cell line] developed at the cell science accelerator at Allen Institute (allencell.org/cell-catalog) and available through Coriell.
Primary publication: Roberts, B. et al. (2017). Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Molecular Biology of the Cell, 28(21). https://doi.org/10.1091/mbc.e17-03-0209.
Plasmids
In text: [Name and number of plasmid] developed at the cell science accelerator at Allen Institute (allencell.org/cell-catalog) and available through AddGene.
In acknowledgements: Acknowledge the cell science accelerator at Allen Institute for developing plasmid(s) used in the work.
Follow this formula for additional lab resources, including those provided to you directly by collaborators at the Allen Institute.
