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File types


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).

Image information

File extension: .csv

Image information (e.g. image dimensions) extracted during preprocessing

CSV file with image file name as index (Image column) and the following columns:

Column Description Type
image Unique image file name Text
width_px Image width, in pixels Numeric
height_px Image height, in pixels Numeric
num_channels Number of image channels Numeric

Further columns may be added by modality-specific preprocessing commands.


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).

Object masks

File extension: .tiff

Grayscale images, 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

Object data

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.

Object neighbors

File extension: .csv

List of directed edges defining a spatial object neighborhood graph

CSV file (one per image) with no index and three columns (Object, Neighbor, Distance)

Undirected graphs

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