draft template-builder tutorial #252
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Thanks @alessandrofelder!
I think my main feedback is that we should add more insructions to the brainglobe-space reorientation step. It's unclear how one would determine the source orientation is PLS by looking at the image in napari. I mean, I know how to do it, but would collaborators be able to do the same based on our instructions?
Other than that, this tutorial gave me some ideas to help streamline it:
- publish the package on PyPI, to make installation easier
- Maybe add a "downsample widget" at the top. It would allow you to choose your image path on disk (without loading it in napari), source/target resolutions, and path for the downsample image. Clicking a button would downsample an image, save to to disk, and load the downsample stack in napari (or perhaps there should be two buttons).
| Brain templates are an average of many brain images. To compute this average, it is highly beneficial to roughly pre-align individual brain images. This makes the averaging a lot faster and more reliable. | ||
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| The `brainglobe-template-builder` tool provides a Graphical User Interface to pre-align sample images to be used for template building later. It's an early work-in-progress tool, so you will have to install it from | ||
| Githubm via the command `pip install git+https://github.com/brainglobe/brainglobe-template-builder`. We recommend doing this in a separate conda environment. |
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Typo: "Githubm".
Also probably we should just release the package on pip, to make the installation easier. But this can also be done later.
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Still need to change the icon image in the index! |
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| You can now move along each image axis and determine which anatomical axes this approximately corresponds to. | ||
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| In our case, moving upwards along the dimension slider (axis 0) goes from posterior to anterior, so the first letter of orientation is P. |
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Maybe phras it as "progressing along the dimension slider (axis 0)". I would avoid mentioning "upwards", "forwards" or "rightwards" here, to avoid confusion with the actual image or anatomy directions
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I think the dropdown is fine for now, just made a few suggestions on wording.
Long term, we do need a separate tutorial for this I think, because it concerns brainglobe as a whole.
Maybe that tutorial could be about our space convention, how to identify your sample space (in napari), and how to change it to the brainglobe space (using the corresponding brainglobe-space package).
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I've also opened an issue to remind ourselves to publish template-builder on PyPI. |
Description
What is this PR
Why is this PR needed?
To improve and accelerate our template-building process, we would like to provide our anatomist collaborators with a tutorial on how to pre-process their data through a GUI.
What does this PR do?
Adds a
template-buildertutorial.