File types

Panel

File extension: .csv

User-provided list of channels present in the images (in order)

Comma-separated values (CSV) file with column headers and no index

Column	Description	Type	Required?
`channel`	Unique channel ID, e.g. metal isotope	Text	yes
`name`	Unique channel name, e.g. antibody target (can be empty only for rows with `keep=0`)	Text or empty	yes
`keep`	Whether the channel is present in preprocessed images (if column is absent, all channels are assumed present)	Boolean (`0` or `1`)	no
`ilastik`	Group label for creating steinbock Ilastik images (if column is absent, all channels are used separately)	Numeric or empty	no
`deepcell`	Group label for DeepCell segmentation (if column is absent, all channels are used separately)	Numeric or empty	no

The steinbock panel allows for further arbitrary columns.

File extension: .tiff

Multi-channel images, where each channel corresponds to a panel entry

Tag Image File Format (TIFF) images of any data type in CYX dimension order

Image data type

Unless explicitly mentioned, images are converted to 32-bit floating point upon loading (without rescaling).

File extension: .tiff

Color images, with one color per class encoding the probability of pixels belonging to that class

16-bit unsigned integer TIFF images in YXS dimension order, same YX ratio as source image

Probability image size

The size of probability images may be different from the original images (see Ilastik pixel classification).

File extension: .tiff

Grayscale image, with one unique value per object ("object ID", 0 for background)

16-bit unsigned integer TIFF images in YX dimension order, same YX shape as source image

File extension: .csv

Object measurements (e.g. mean intensities, morphological features)

CSV file with object IDs as index (Object column) and feature/channel names as columns

Combined object data

For data containing measurements from multiple images, a combined index of image name and object ID is used.

File extension: .csv

Pixel distances between objects (e.g. Euclidean centroid distances)

Symmetric CSV file (one per image) with object IDs as both index (Object column) and columns

File extension: .csv

List of directed edges defining a spatial object neighborhood graph

CSV file (one per image) with no index and two columns (Object1, Object2)

Each row defines an edge from object with ID Object1 to object with ID Object2

Undirected graphs

For undirected graphs, each edge appears twice (one edge per direction)