# 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