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55 changes: 37 additions & 18 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,35 +1,52 @@
# QuBaLab

This is a Python package for exploring quantitative bioimage analysis... *especially* (but not exclusively) in
This is a Python package for exploring quantitative bioimage analysis...
*especially* (but not exclusively) in
combination with QuPath (https://qupath.github.io/).

The name comes from **Quantitative Bioimage Analysis Laboratory**.
This is chosen to be reminiscent of QuPath (*Quantitative Pathology*), but recognizes that neither is really restricted
to pathology.
This is chosen to be reminiscent of QuPath (*Quantitative Pathology*),
but recognizes that neither is really restricted to pathology.

## Goals
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QuBaLab isn't QuPath - they're just good friends.

* **QuPath** is a user-friendly Java application for bioimage analysis, which has some especially nice features for
handling whole slide and highly-multiplexed images. But lots of bioimage analysis researcher is done in Python,
and is hard to integrate with QuPath.
* **QuBaLab**'s main aim is to help with this, by providing tools to help exchange data between QuPath and Python
*without any direct dependency on QuPath and Java*. It therefore doesn't require QuPath to be installed, and
can be used entirely from Python.

QuBaLab doesn't share code with QuPath, but is uses many of the same conventions for accessing images and
representing objects in a GeoJSON-compatible way.
By using the same custom fields for things like measurements and classifications, exchanging data is much easier.
* **QuPath** is a user-friendly Java application for bioimage analysis,
which has some especially nice features for
handling whole slide and highly-multiplexed images.
But lots of bioimage analysis research is done in Python,
and is hard to integrate with QuPath.
* **QuBaLab**'s main aim is to help with this, by providing tools to help
exchange data between QuPath and Python
*without any direct dependency on QuPath and Java*.
It therefore doesn't require QuPath to be installed, and
can be used entirely from Python.

QuBaLab doesn't share code with QuPath, but is uses many of the same conventions
for accessing images and representing objects in a GeoJSON compatible way.
By using the same custom fields for things like measurements and classifications,
exchanging data is much easier.

[paquo](https://paquo.readthedocs.io/en/latest/index.html) is an existing library
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linking Python and QuPath that provides a pythonic interface to QuPath.
It makes creating and working with QuPath projects intuitive and easy
for Python programmers. We think paquo is great, and don't want to replace it!
The linkage that QuBaLab provides between Python and QuPath is more
resource-intensive and slow, with the tradeoff that it is (we hope) more
convenient to dip in and out of.

## Getting started

You can find the documentation on https://qupath.github.io/qubalab-docs/.

This project contains the QuBaLab package in the `qubalab` folder. Take a look at the *Installation* section to install it.
This project contains the QuBaLab package in the `qubalab` folder.
Take a look at the *Installation* section to install it.

Some notebooks present in the `notebooks` folder show how to use the QuBaLab package. If you want to run them, you can take a look at the *Development* section.
If you just want to go through them, look at the [documentation](https://qupath.github.io/qubalab-docs/notebooks.html).
Some notebooks in the `notebooks` folder demonstrate how to use QuBaLab.
If you want to run them, you can take a look at the *Development* section.
If you just want to browse the content in them, look at the
[documentation](https://qupath.github.io/qubalab/notebooks.html).

## Installation

Expand Down Expand Up @@ -65,6 +82,8 @@ pytest # to run unit tests
## OpenSlide support

OpenSlide support relies on having OpenSlide binaries installed at a system
level. Therefore not all aspects of OpenSlide will work consistently across
level. Therefore, not all aspects of OpenSlide will work consistently across
platforms, as the versions available from package managers or from OpenSlide
directly may vary between operating systems.
directly may vary between operating systems. We hope that this will be resolved
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shortly with the release of OpenSlide 4.0.0 binaries in the
[openslide-bin](https://pypi.org/project/openslide-bin/) package.
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