3c14168878
- less restrictive dependency versions - some extra features and bugfixes for movie writing - make python tests work again
105 lines
3.0 KiB
Markdown
105 lines
3.0 KiB
Markdown
# ndbioimage
|
|
[](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
|
|
|
|
## Work in progress
|
|
Rust rewrite of python version. Read bio image formats using the bio-formats java package.
|
|
[https://www.openmicroscopy.org/bio-formats/](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](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47) 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](https://www.openmicroscopy.org/bio-formats/) 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)?;
|
|
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);
|
|
```
|
|
|
|
```
|
|
use ndarray::Array2;
|
|
use ndbioimage::Reader;
|
|
|
|
let path = "/path/to/file";
|
|
let reader = Reader::new(&path, 0)?;
|
|
let view = reader.view();
|
|
let view = view.max_proj(3)?;
|
|
let array = view.as_array::<u16>()?
|
|
```
|
|
|
|
### 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
|