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‎.doctrees/documentation/brainglobe-utils/image_io.doctree

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‎.doctrees/documentation/brainrender/usage/using-your-data/index.doctree

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‎.doctrees/documentation/index.doctree

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‎_sources/documentation/brainglobe-utils/image_io.md.txt

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# image_io
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`image_io` provides various options to load and save image data.
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It supports common formats like `tiff`, `nrrd` and `nifti`.
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## Installation
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`image_io` is provided as part of `brainglobe_utils` which comes with the one-line BrainGlobe install (`pip install brainglobe`).
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It will also be fetched by most of our tools if you decide to install them as standalone.
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## Loading images
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All options to load images are provided under `brainglobe_utils.image_io.load`.
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For example, the general purpose `load_any` function which can load many common file formats:
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```python
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from brainglobe_utils.image_io import load
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load.load_any('mydata.tif')
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```
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There are also functions specific to particular file formats:
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```python
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from brainglobe_utils.image_io import load
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# tiff
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load.load_img_stack('mydata.tif', x_scaling_factor=1, y_scaling_factor=1, z_scaling_factor=1)
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# directory containing a sequence of 2D tiffs
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load.load_from_folder('/path/to/dir')
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# nrrd
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load.load_nrrd('mydata.nrrd')
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# nifti
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load.load_nii('mydata.nii')
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```
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## Saving images
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All options to save images are provided under `brainglobe_utils.image_io.save`.
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For example, the general purpose `save_any` function which can save a numpy array to many common file formats:
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```python
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from brainglobe_utils.image_io import save
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save.save_any(my_array, 'mydata.tif')
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```
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There are also functions specific to particular file formats:
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```python
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from brainglobe_utils.image_io import save
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# tiff
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save.to_tiff(my_array, 'mydata.tif')
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# directory containing a sequence of 2D tiffs
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save.to_tiffs(my_array, '/path/to/dir/prefix')
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# nrrd
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save.to_nrrd(my_array, 'mydata.nrrd')
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# nifti
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save.to_nii(my_array, 'mydata.nii')
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```

‎_sources/documentation/brainrender/usage/using-your-data/index.md.txt

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Given the popularity of python for scientific research, there are tools to load almost all data formats. These include
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numpy to load `.npy` files, `tiffiles` for `.tiff` etc. BrainGlobe provides a general purpose software tool for
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loading and saving image data ([imio](https://github.com/brainglobe/imio)). You can use `imio` to load most types of
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loading and saving image data ([image_io](/documentation/brainglobe-utils/image_io)). You can use `image_io` to load most types of
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data (e.g. `.nrrd`, `.tiff`, `.nifti` etc), e.g.:
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```python
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from imio import load
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from brainglobe_utils.image_io import load
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load.load_any('mydata.tif')
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```
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‎_sources/documentation/index.md.txt

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brainglobe-atlasapi/index
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brainglobe-space/index
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brainglobe-utils/citation-module
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brainglobe-utils/image_io
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brainreg/index
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brainglobe-segmentation/index
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brainglobe-workflows/index

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