Crate imc_rs

This library provides a means of accessing imaging mass cytometry (Fluidigm) data stored in the (*.mcd) format.

Example

To run this example, make sure to first download the test file 20200612_FLU_1923.mcd to the test/ folder.

extern crate imc_rs;

use imc_rs::MCD;
use std::io::BufReader;
use std::fs::File;

fn main() {
    let filename = "../test/20200612_FLU_1923.mcd";

    let mcd = MCD::from_path(filename).unwrap();

    // Optionally we can load/create the .dcm file for fast access to images
    let mcd = mcd.with_dcm().unwrap();

}

Modules

• convert
  Convert .mcd file to .dcm file for faster access to data.
• error
  Errors associated with parsing IMC data
• halo
  Provides methods for reading in cell segmentation data from Halo
• transform
  Transformations (e.g. affine) used for converting

Structs

• Acquisition
  Acquisition represents a single region analysed by IMC.
• AcquisitionChannel
  AcquisitionChannel represents a single channel acquired, forming part of an acquisition
• BoundingBox
  Represents a bounding rectangle
• ChannelImage
  Represents a channel image (stored as a vector of f32). If the run was stopped mid acquisition width*height != valid_pixels
• MCD
  Represents a imaging mass cytometry (*.mcd) file.
• OpticalImage
  Represents property of having an optical image
• Panorama
  Represents a panorama (containing one or more acquisitions)
• Region
  Represents a region of an image (in pixels)
• Slide
  Represents a slide (contains multiple panoramas) in the *.mcd format

Enums

• AcquisitionIdentifier
  AcquisitionIdentifier is a way of identifying a specific acquisition
• ChannelIdentifier
  ChannelIdentifier describes how a channel can be identified

Traits

• Acquisitions
  Trait describing a collection of acquisitions and providing methods to summarise the collection (e.g. to get the list of channels)
• OnSlide
  Represents an image which is acquired on a slide
• Print
  Print to writer trait