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Preprocessing

In this step, image data will be prepared for processing with steinbock.

Various sources for raw data are supported by steinbock, each of which is described in the following. If you miss support for an imaging modality, please consider filing an issue on GitHub.

Optional preprocessing

The steinbock framework natively supports input images saved in Tag Image File Format (TIFF), see File types. If you already have preprocessed TIFF files, you can directly use those for further processing. If you have preprocessed images in another file format supported by imageio, you need to convert them to steinbock-compatible TIFF files first, see External images.

Computational resources

Unless specified otherwise, steinbock converts all input images to 32-bit floating point images upon loading, see File types. For large images, this may exhaust a system's available random access memory (RAM). In these situations, it is recommended to run all operations on image tiles, see mosaics.

Imaging Mass Cytometry (IMC)

Preprocessing of IMC data consists of two steps:

  1. Create a steinbock panel file and, optionally, edit it to select channels
  2. Extract images from .mcd/.txt files according to the created steinbock panel file

Panel-based image extraction

The steinbock panel determines the presence and order of channels in the extracted images.

Panel creation

A steinbock panel file contains information about the channels in an image, such as channel ID (e.g. metal tag), channel name (e.g. antibody target), or whether a channel will be used in certain tasks (e.g. classification, segmentation). Multiple options exist for creating a steinbock panel file for IMC applications:

  • Manual steinbock panel file creation, following the steinbock panel format specification
  • Automatic steinbock panel file creation from metadata embedded in raw MCD/TXT files
  • Conversion from an "IMC panel file" in IMC Segmentation Pipeline1 format (undocumented)

Panel file types

The steinbock panel file is different from the "IMC panel file" used in the original IMC Segmentation Pipeline1 in that it is ordered (i.e., the channel order in the panel matches the channel order in the images) and only requires channel and name columns (see File types). By default, channels in a steinbock panel file generated from IMC raw data are sorted by mass. As the steinbock panel format allows for further arbitrary columns, unmapped columns from an original "IMC panel" will be "passed through" to the generated steinbock panel.

When manually creating the steinbock panel file, no further actions are required; proceed with image conversion. Otherwise, to create a steinbock panel file for IMC data processing:

steinbock preprocess imc panel

This will create a steinbock panel at the specified location (defaults to panel.csv) as follows:

  • If an IMC panel file (in IMC Segmentation Pipeline1 format, undocumented) exists at the specified location (defaults to raw/panel.csv), it is converted to the steinbock panel format.
  • If no IMC panel file was found, the steinbock panel is created based on all acquisitions in all .mcd files found at the specified location (defaults to raw).
  • If no IMC panel file and no .mcd file were found, the steinbock panel is created based on all .txt files found at the specified location (defaults to raw).

Different panels

In principle, IMC supports acquiring a different panel for each .mcd/.txt file and acquisition. When creating a steinbock panel from .mcd/.txt files, the created panel will contain all targets found in any of the input files. During image conversion (see below), only targets marked as keep=1 in the panel file will be retained; imaging data with missing channels (identified by the channel column in the panel file) are skipped.

Image conversion

To convert .mcd/.txt files in the raw data directory to TIFF and filter hot pixels:

steinbock preprocess imc images --hpf 50

This will extract images from raw files (source directory defaults to raw) and save them at the specified location (defaults to img). Each image corresponds to one acquisition in one file, with the image channels filtered (keep column) and sorted according to the steinbock panel file at the specified location (defaults to panel.csv). For corrupted .mcd files, steinbock will try to recover the missing acquisitions from matching .txt files. In a second step, images from unmatched .txt files are extracted as well.

Furthermore, this commands also creates an image information table as described in File types. In addition to the default columns, the following IMC-specific columns will be added:

  • source_file: the raw .mcd/.txt file name
  • recovery_file: the corresponding .txt file name, if available
  • recovered: True if the .mcd acquisition was recovered from the corresponding .txt file
  • Acquisition-specific information (only for images extracted from .mcd files):
    • acquisition_id: numeric acquisition ID
    • acquisition_description: user-specified acquisition description
    • acquisition_posx_um, acquisition_posy_um: start position, in micrometers
    • acquisition_width_um, acquisition_height_um: dimensions, in micrometers

IMC file matching

Matching of .txt files to .mcd files is performed by file name: If a .txt file name starts with the file name of an .mcd file (without extension) AND ends with _{acquisition}.txt, where {acquisition} is the numeric acquisition ID, it is considered matching that particular acquisition from the .mcd file.

ZIP archives

If .zip archives are found in the raw data directory, contained .txt/.mcd files will be automatically extracted to a temporary directory, unless disabled using the --no-unzip command-line option. After image extraction, this temporary directory and its contents will be removed.

After image extraction, if the --hpf option is specified, the images are filtered for hot pixels. The value of the --hpf option (50 in the example above) determines the hot pixel filtering threshold.

Hot pixel filtering

Hot pixel filtering works by comparing each pixel to its 8-neighborhood (i.e., neighboring pixels at a Chebyshev distance of 1). If the difference (not: absolute difference) between the pixel and any of its 8 neighbor pixels exceeds a hot pixel filtering threshold, the pixel is set to the maximum neighbor pixel value ("hot pixel-filtered"). In the original implementation of the IMC Segmentation Pipeline1, a hot pixel filtering threshold of 50 is recommended.

External images

External images are images preprocessed externally (i.e., without steinbock) that are saved in an image format supported by imageio.

For convenience, to create a template panel file based on external image data stored at the specified location (defaults to external):

steinbock preprocess external panel

To convert external image data to steinbock-supported TIFF files (see File types) and save them to the specified location (defaults to external):

steinbock preprocess external images

  1. Zanotelli et al. ImcSegmentationPipeline: A pixel classification-based multiplexed image segmentation pipeline. Zenodo, 2017. DOI: 10.5281/zenodo.3841961. ↩↩↩↩