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Datasets

  • 60x timelapse images of tagged lines "after" EMT, "sandwich" dataset
  • Actin compression simulation dataset

    Overview

    This dataset contains simulated data of actin filaments using the monomer-scale model ReaDDy and fiber-scale model Cytosim.

    Simulation conditions test compression of a single 500 nm actin filament at different velocities, as well as control simulations with no compression.

    Compression simulations use the prefix ACTIN_COMPRESSION_VELOCITY; control simulations use the prefix ACTIN_NO_COMPRESSION.

    Compression simulation keys include the following:

    • 0047 = 4.7 μm/s
    • 0150 = 15 μm/s
    • 0470 = 47 μm/s
    • 1500 = 150 μm/s

    For ReaDDy, the actin filament is composed of particles, each representing an actin monomer, initialized based on measurements from an actin crystal structure. Compression was implemented by linearly displacing the three monomers at the pointed end for one time step and then allowing the structure to relax for nine time steps, until the fiber was compressed to 350 nm. Each simulation condition contains 5 replicates.

    For Cytosim, the actin filament is modeled as a 500 nm fiber anchored by two fiber-binding linkers spaced 10 nm apart at each end. The linkers on one of the ends were translated linearly for one time step and allowed to relax for nine time steps, until the fiber was compressed to 350 nm. Each simulation condition contains 5 replicates, with replicates corresponding to random seeds 1, 2, 3, 4, and 5.

    Usage

    For documentation on how to use and interact with this dataset please refer to https://docs.quiltdata.com/walkthrough/getting-data-from-a-package.

    License

    For questions on licensing please refer to https://www.allencell.org/terms-of-use.html.

  • EMC

    We have some preliminary data on different ECM to drive lumenoid formation

  • Hybrid model simulations: Hamiltonian terms dataset

    Overview

    This dataset contains simulated data from the Hamiltonian terms series using the hybrid agent-based modeling framework ARCADE v3.1.4.

    Simulation conditions test different combinations of Cellular Potts Model Hamiltonian terms. All simulations use the prefix HAMILTONIAN_TERMS_FOV. Simulation keys include the following:

    • VA = Hamiltonian terms include volume constraint and adhesion terms
    • VAU = Hamiltonian terms include volume constraint, adhesion terms, and differential substrate adhesion

    Simulations are run with 10 replicates (random seeds 0 - 9) initialized from select FOVs by placing the filtered and sampled cell and nuclear shapes in the center of a 500 μm x 500 μm x 500 μm environment (for VA) or the bottom of a 1 mm x 1 mm x 125 μm environment immediately above the substrate (for VAU) using a spatial resolution of 1 μm/voxel. Simulations are run for 5,760 ticks at a temporal resolution of 1 minute/tick representing 4 days of growth. All adhesion parameters (cell-cell, cell-media, subcellular, and cell-substrate) are set to baseline value of 50. Snapshots are taken every 5 minutes (5 ticks).

    The dataset has the following structure:

    .
├── analysis
│   └── analysis.BASIC_METRICS
│       └── (name)_(superkey).BASIC_METRICS.csv
├── data
│   ├── data.CELLS
│   │   └── (name)_(key)_(seed).CELLS.tar.xz
│   └── data.LOCATIONS
│       └── (name)_(key)_(seed).LOCATIONS.tar.xz
├── inits
│   ├── inits.CELLS
│   │   └── (name)_(seed).CELLS.json
│   └── inits.LOCATIONS
│       └── (name)_(seed).LOCATIONS.json
├── results
│   └── (name)_(key)_(seed).csv
├── setups
│   └── (name).xml
├── simulations
│   └── (name)_(key).json
└── README.md
    • analysis = various analysis files
      • analysis.BASIC_METRICS = all results compiled into files grouped by superkey
    • data = compressed simulation outputs for each condition and seed
      • data.CELLS = individual cell agent data for each tick (including cell id, parent id, population, age, number of divisions, cell state and phase, volume, and height)
      • data.LOCATIONS = individual location data for each tick (including cell id and list of voxels belonging to the cell)
    • inits = simulation initialization files for each seed
    • results = tidy formatted data parsed from simulation outputs, for each condition and seed
    • setups = all simulation setup files
    • simulations = simulation summary output files for each condition

    Usage

    For documentation on how to use and interact with this dataset please refer to https://docs.quiltdata.com/walkthrough/getting-data-from-a-package.

    License

    For questions on licensing please refer to https://www.allencell.org/terms-of-use.html.

  • Released EMT dataset

    Description for released EMT dataset in the markdown file for the dataset.

  • Released nucmorph data, included pre-calculated PCs.
  • test dataset

    A sample dataset for development and testing.

Cell Lines

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