Dataset Fields

Definitions, examples, and units for each field required for processing or produced.

CellId

  • Description: A unique identifier for a cell. Can be an integer, string, or other, but must be serializable and unique.

  • Example(s): 1, 2, 3, f0e3ac9a-5f20-4c40-bc6b-9c7c0a7e026d

  • Units: None

CellIndex

  • Description: The integer value used in a segmentation image to indicate that a voxel belongs to a specific cell.

  • Example(s): 1, 2, 3

  • Units: None

FOVId

  • Description: A unique identifier for a Field-of-View image. Can be an integer, string, or other, but must be serializable and unique.

  • Example(s): 1, 2, 3, f0e3ac9a-5f20-4c40-bc6b-9c7c0a7e026d

  • Units: None

SourceReadPath

  • Description: The path to reader a raw microscopy image file. This file should contain at least four channels (DNA, membrane, tagged structure, and brightfield).

  • Example(s): /allen/aics/modeling/jacksonb/data/example_raw.czi

  • Units: None

NucleusSegmentationReadPath

  • Description: The path to read a file that contains an channel with a nucleus segmentation. This file is usually generated by segmenting the DNA channel from a raw microscopy image.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_nuc_seg.ome.tiff

  • Units: None

MembraneSegmentationReadPath

  • Description: The path to read a file that contains an channel with a membrane segmentation. This file is usually generated by segmenting the membrane channel from a raw microscopy image.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_memb_seg.ome.tiff

  • Units: None

ChannelIndexDNA

  • Description: The integer index of the DNA channel in a raw microscopy image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

ChannelIndexMembrane

  • Description: The integer index of the membrane channel in a raw microscopy image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

ChannelIndexMembrane

  • Description: The integer index of the membrane channel in a raw microscopy image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

ChannelIndexStructure

  • Description: The integer index of the structure channel in a raw microscopy image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

ChannelIndexBrightfield

  • Description: The integer index of the brightfield channel in a raw microscopy image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

ChannelIndexNucleusSegmentation

  • Description: The integer index of the nucleus segmentation channel in a segmentation file image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

ChannelIndexMembraneSegmentation

  • Description: The integer index of the membrane segmentation channel in a segmentation file image after it has been read into memory.

  • Example(s): 0, 1, 2, 3

  • Units: None

StandardizedFOVPath

  • Description: The path to read a standardized FOV image file. This file is generated from the “StandardizeFOVArray” step.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_fov_array.ome.tiff

  • Units: None

CellFeaturesPath

  • Description: The path to read a cell features JSON file. This file is generated from the “SingleCellFeatures” step.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_cell_feats.json

  • Units: None

CellImage3DPath

  • Description: The path to read a normalized and bounded 3D single cell image. This file is generated from the “SingleCellImages” step.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_single_cell.ome.tiff

  • Units: None

CellImage2DAllProjectionsPath

  • Description: The path to view a normalized and bounded 2D single cell image where all axis projections can be seen in a single image. This file is generated from the “SingleCellImages” step.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_single_cell_all_proj.png

  • Units: None

CellImage2DYXProjectionPath

  • Description: The path to view a normalized and bounded 2D single cell image where only the YX axis projection can be seen in a single image. This file is generated from the “SingleCellImages” step.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_single_cell_yx_proj.png

  • Units: None

DiagnosticSheetPath

  • Description: The path to view a diagnostic or “contact” sheet of the cells produced by the pipeline grouped by metadata. Useful for quality control. This file is generated from the “DiagnosticSheets” step.

  • Example(s): /allen/aics/modeling/jacksonb/data/example_fov_dianostics.png

  • Units: None