imcjs

Parse Imaging Mass Cytometry (IMC) MCD and TXT files in the browser or with Node

Mimics the Python API provided by readimc.

imcjs depends only on basic, browser-compatible XML parsers.

Quickstart

Install: npm install

Testing: npm run test

Build: npm run build

Basic Usage

Node

import { MCDFile } from "imcjs";

const mcd = await MCDFile.fromPath(string_path_to_mcd);

Browser File API

import { MCDFile } from "imcjs";


function handleFileUpload(e) {

    let filesUploaded = Array.from(e.target.files);
    const mcd = await MCDFile.fromFile(filesUploaded[0]);

}

From remote URL

NOTE: this feature is experimental and not part of the original Python API.

import { MCDFile } from "imcjs";

const mcd = await MCDFile.fromURL("https://borealisdata.ca/api/access/datafile/833251");

Read an MCD acquisition

# Read the first acquisition, and view the array data and shape (C, H, W)

const slides = await mcd.getSlides();
const acqRead = await mcd.readAcquisition(slides[0].acquisitions[0]);
console.log(acqRead.data, acqRead.shape);

Development

Minimum version recommended:

• Node: v20+
• npm: v11+
• tsc: v7+