Crate imc_rs

Expand description

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§