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Wim Pomp
2023-06-29 14:34:54 +02:00
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README.md
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# ndbioimage - Work in progress # ndbioimage - Work in progress
Exposes (bio) images as a numpy ndarray-like-object, but without loading the whole 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 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 and stored in an ome structure. Additionally, it can automatically calculate an affine
transform that corrects for chromatic abberrations etc. and apply it on the fly to the image. transform that corrects for chromatic abberrations etc. and apply it on the fly to the image.
Currently supports imagej tif files, czi files, micromanager tif sequences and anything Currently, supports imagej tif files, czi files, micromanager tif sequences and anything
bioformats can handle. bioformats can handle.
## Installation ## Installation
```
pip install ndbioimage@git+https://github.com/wimpomp/ndbioimage.git pip install ndbioimage@git+https://github.com/wimpomp/ndbioimage.git
```
Optionally:
https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bioformats_package.jar
## Usage ## Usage
- Reading an image file and plotting the frame at channel=2, time=1 - Reading an image file and plotting the frame at channel=2, time=1
```
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from ndbioimage import Imread from ndbioimage import Imread
with Imread('image_file.tif', axes='ctxy', dtype=int) as im: with Imread('image_file.tif', axes='ctxy', dtype=int) as im:
plt.imshow(im[2, 1]) plt.imshow(im[2, 1])
```
- Showing some image metadata - Showing some image metadata
```
from ndbioimage import Imread from ndbioimage import Imread
from pprint import pprint from pprint import pprint
with Imread('image_file.tif') as im: with Imread('image_file.tif') as im:
pprint(im) pprint(im)
```
- Slicing the image without loading the image into memory - Slicing the image without loading the image into memory
```
from ndbioimage import Imread from ndbioimage import Imread
with Imread('image_file.tif', axes='cztxy') as im: with Imread('image_file.tif', axes='cztxy') as im:
sliced_im = im[1, :, :, 100:200, 100:200] 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 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 - Converting (part) of the image to a numpy ndarray
```
from ndbioimage import Imread from ndbioimage import Imread
import numpy as np import numpy as np
with Imread('image_file.tif', axes='cztxy') as im: with Imread('image_file.tif', axes='cztxy') as im:
array = np.asarray(im[0, 0]) array = np.asarray(im[0, 0])
```
## Adding more formats ## Adding more formats
Readers for image formats subclass Imread. When an image reader is imported, Imread will Readers for image formats subclass Imread. When an image reader is imported, Imread will

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pyproject.toml
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[tool.poetry] [tool.poetry]
name = "ndbioimage" name = "ndbioimage"
version = "2023.6.0" version = "2023.6.1"
description = "Bio image reading, metadata and some affine registration." description = "Bio image reading, metadata and some affine registration."
authors = ["W. Pomp <w.pomp@nki.nl>"] authors = ["W. Pomp <w.pomp@nki.nl>"]
license = "GPLv3" license = "GPLv3"