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 |
cellpose |
Group label for Cellpose segmentation (if column is absent, all channels are used separately) |
Numeric or empty | no |
The steinbock panel allows for further arbitrary columns.
Images
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.
Probabilities
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)