From 9c59328547fb163be95dcd1d4aec6d80d49d41df Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 12 Dec 2023 14:31:18 +0000 Subject: [PATCH 1/3] Simplify and update readme --- README.md | 31 +++++++++++++++---------------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 0f548ee..ad61208 100644 --- a/README.md +++ b/README.md @@ -2,28 +2,27 @@ [![PyPI](https://img.shields.io/pypi/v/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation) [![Wheel](https://img.shields.io/pypi/wheel/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation) [![Development Status](https://img.shields.io/pypi/status/brainglobe-segmentation.svg)](https://github.com/brainglobe/brainglobe-segmentation) -[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)]( - https://github.com/brainglobe/brainglobe-segmentation/actions) -[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black) +[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)](https://github.com/brainglobe/brainglobe-segmentation/actions) +[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainglobe-segmentation) +[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black) [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe) # brainglobe-segmentation -Segmentation of 1/2/3D brain structures in a common anatomical space - -`brainglobe-segmentation` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing segmentation -of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain -region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)). -`brainglobe-segmentation` is the successor to [`brainreg-segment`](https://github.com/brainglobe/brainreg-segmentation). - -`brainglobe-segmentation` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/). - +Segmentation of anatomical structures in a common coordinate space + ## Installation +**PyPI** +``` +pip install brainglobe-segmentation +``` -brainglobe-segmentation comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://brainglobe.info/documentation/brainreg/index.html). - -brainglobe-segmentation can be installed on it's own (`pip install brainglobe-segmentation`), but you will need to register your data with brainreg first. +**conda** +``` +conda install brainglobe-segmentation -c conda-forge +``` +N.B. Your data will need to be registered to an anatomical atlas first. ## Usage See [user guide](https://brainglobe.info/documentation/brainglobe-segmentation/index.html). @@ -32,7 +31,7 @@ If you have any questions, head over to the [image.sc forum](https://forum.image ## Contributing -Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html). +Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/community/developers/index.html). ### Citing brainglobe-segmentation From e1d9c553bde261635eaeb330d53f86eee9ee350d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 12 Dec 2023 14:32:00 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ad61208..bb4d0a7 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ # brainglobe-segmentation Segmentation of anatomical structures in a common coordinate space - + ## Installation **PyPI** ``` @@ -22,7 +22,7 @@ pip install brainglobe-segmentation conda install brainglobe-segmentation -c conda-forge ``` -N.B. Your data will need to be registered to an anatomical atlas first. +N.B. Your data will need to be registered to an anatomical atlas first. ## Usage See [user guide](https://brainglobe.info/documentation/brainglobe-segmentation/index.html). From 8bba943fd2da934782f1840327e03578115c1abf Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 12 Dec 2023 15:10:32 +0000 Subject: [PATCH 3/3] Update README.md Co-authored-by: Will Graham <32364977+willGraham01@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bb4d0a7..3d4b127 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ pip install brainglobe-segmentation **conda** ``` -conda install brainglobe-segmentation -c conda-forge +conda install -c conda-forge brainglobe-segmentation ``` N.B. Your data will need to be registered to an anatomical atlas first.