ndbioimage

Work in progress

Rust rewrite of python version. Read bio image formats using the bio-formats java package. https://www.openmicroscopy.org/bio-formats/

Exposes (bio) images as a numpy ndarray-like object, but without loading the whole image into memory, reading from the file only when needed. Some metadata is read and stored in an ome structure. Additionally, it can automatically calculate an affine transform that corrects for chromatic aberrations etc. and apply it on the fly to the image.

Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything bioformats can handle.

Installation

pip install ndbioimage

Installation with option to write mp4 or mkv:

Work in progress! Make sure ffmpeg is installed.

pip install ndbioimage[write]

Usage

Python

• Reading an image file and plotting the frame at channel=2, time=1

import matplotlib.pyplot as plt
from ndbioimage import Imread
with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
    plt.imshow(im[2, 1])

• Showing some image metadata

from ndbioimage import Imread
from pprint import pprint
with Imread('image_file.tif') as im:
    pprint(im)

• Slicing the image without loading the image into memory

from ndbioimage import Imread
with Imread('image_file.tif', axes='cztyx') as im:
    sliced_im = im[1, :, :, 100:200, 100:200]

sliced_im is an instance of Imread which will load any image data from file only when needed

• Converting (part) of the image to a numpy ndarray

from ndbioimage import Imread
import numpy as np
with Imread('image_file.tif', axes='cztyx') as im:
    array = np.asarray(im[0, 0])

Rust

use ndarray::Array2;
use ndbioimage::Reader;

let path = "/path/to/file";
let reader = Reader::new(&path, 0).unwrap();
println!("size: {}, {}", reader.size_y, reader.size_y);
let frame = reader.get_frame(0, 0, 0).unwrap();
if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
    println!("{:?}", arr);
} else {
    println!("could not convert Frame to Array<i8>");
}
let xml = reader.get_ome_xml().unwrap();
println!("{}", xml);

Command line

ndbioimage --help: show help
ndbioimage image: show metadata about image
ndbioimage image -w {name}.tif -r: copy image into image.tif (replacing {name} with image), while registering channels
ndbioimage image -w image.mp4 -C cyan lime red copy image into image.mp4 (z will be max projected), make channel colors cyan lime and red

Adding more formats

Readers for image formats subclass AbstractReader. When an image reader is imported, Imread will automatically recognize it and use it to open the appropriate file format. Image readers are required to implement the following methods:

• staticmethod _can_open(path): return True if path can be opened by this reader
• __frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file

Optional methods:

• get_ome: reads metadata from file and adds them to an OME object imported from the ome-types library
• open(self): maybe open some file handle
• close(self): close any file handles

Optional fields:

• priority (int): Imread will try readers with a lower number first, default: 99
• do_not_pickle (strings): any attributes that should not be included when the object is pickled, for example: any file handles

TODO

• more image formats