diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index cbc909cf..64693929 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,5 +1,5 @@ FOR CONTRIBUTOR: -* [ ] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. +* [ ] - I have read the [CONTRIBUTING.md](https://github.com/BMCV/galaxy-image-analysis/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the galaxy-image-analysis repo. * [ ] - License permits unrestricted use (educational + commercial) * [ ] - This PR adds a new tool or tool collection * [ ] - This PR updates an existing tool or tool collection diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..1ef1be31 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,8 @@ +Code of Conduct +=============== + +As part of the Galaxy Community, this project is committed to providing a +welcoming and harassment-free experience for everyone. We therefore expect +participants to abide by our Code of Conduct, which can be found at: + +https://galaxyproject.org/community/coc/ diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..7ad01aa8 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,16 @@ +# Contributing + +This document describes how to contribute to this repository. Pull +requests containing bug fixes, updates, and extensions to the existing +tools and tool suites in this repository will be considered for +inclusion. + +## How to Contribute + +* Make sure you have a [GitHub account](https://github.com/signup/free) +* Make sure you have git [installed](https://help.github.com/articles/set-up-git) +* Fork the repository on [GitHub](https://github.com/BMCV/galaxy-image-analysis/fork) +* Make the desired modifications - consider using a [feature branch](https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches). +* Try to stick to the [Conventions for Tools in the Image Community](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/conventions.md) and the [IUC standards](http://galaxy-iuc-standards.readthedocs.org/en/latest/) whenever you can +* Make sure you have added the necessary tests for your changes and they pass. +* Open a [pull request](https://help.github.com/articles/using-pull-requests) with these changes. diff --git a/README.md b/README.md index 8f19bc52..8a9a6332 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,58 @@ [![Build Status](https://travis-ci.org/BMCV/galaxy-image-analysis.svg?branch=master)](https://travis-ci.org/BMCV/galaxy-image-analysis) +[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.jbiotec.2017.07.019-blue)](https://doi.org/10.1016/j.jbiotec.2017.07.019) +[![Chat on matrix](https://img.shields.io/badge/chat_on-matrix-green)](https://matrix.to/#/#galaxyproject_imaging:matrix.org) -Galaxy Image Analysis -======================== +# Galaxy Image Analysis +Galaxy Image Analysis is mainly developed by the [Biomedical Computer Vision (BMCV) Group](http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html) at Heidelberg University. If you would like to contribute, please see [our contribution instructions](CONTRIBUTING.md). -Galaxy Image Analysis developed by the [Biomedical Computer Vision (BMCV) Group](http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html) at Heidelberg University. +Galaxy Image Analysis is part of the [Image Community in Galaxy](https://imaging.usegalaxy.eu). -If Galaxy Image Analysis helped with the analysis of your data, please do not forget to cite: https://doi.org/10.1016/j.jbiotec.2017.07.019 +If Galaxy Image Analysis helped with the analysis of your data, please do not forget to cite: -Acknowledgment -======================== -This work has been supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI) #031A537C. +## List of Tools on Galaxy Europe + +- [Extract 2D features](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction) +- [Apply anisotropic diffusion](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/anisotropic_diffusion/ip_anisotropic_diffusion) +- [Perform linking in time series (nearest neighbors)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/points_association_nn/ip_points_association_nn) +- [Threshold image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold) +- [Convert binary image to label map](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage) +- [Convert binary image to points (center of masses)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/binaryimage2points/ip_binaryimage_to_points) +- [Perform color decomposition](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/ip_color_deconvolution) +- [Concatenate images or channels](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/concat_channels/ip_concat_channels) +- [Convert image format](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage) +- [Convert binary image to points (point coordinates)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/coordinates_of_roi/ip_coordinates_of_roi) +- [Count objects in label map](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects) +- [Perform curve fitting](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/curve_fitting/ip_curve_fitting) +- [Visualize detections](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/detection_viz/ip_detection_viz) +- [Extract top view](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/wsi_extract_top_view/ip_wsi_extract_top_view) +- [Filter 2D image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard) +- [Filter label map by rules](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features) +- [Perform histogram equalization](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization) +- [Show image info](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo) +- [Perform affine image registration (intensity-based)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/image_registration_affine/ip_image_registration) +- [Convert label map to points (center of masses)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/labelimage2points/ip_labelimage_to_points) +- [Perform affine image registration (landmark-based)](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/landmark_registration/ip_landmark_registration) +- [Perform local thresholding](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_local_threshold/ip_localthreshold) +- [Compute image features](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/mahotas_features/ip_mahotas_features) +- [Merge neighbors in label map](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/mergeneighboursinlabelimage/ip_merge_neighbours_in_label) +- [Overlay images](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images) +- [Permutate image axes](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/permutate_axis/ip_permutate_axis) +- [Convert point coordinates to binary image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/points2binaryimage/ip_points_to_binaryimage) +- [Convert point coordinates to label map](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/points2labelimage/ip_points_to_label) +- [Performs projective transformation with/without labels](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/projective_transformation_points/ip_projective_transformation_points) +- [Performs projective transformation](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/projective_transformation/ip_projective_transformation) +- [Scale image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/ip_scale_image) +- [Compute image segmentation and object detection performance measures](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/segmetrics/ip_segmetrics) +- [Slice image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image) +- [Split label map using morphological operators](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/split_labelmap/ip_split_labelmap) +- [Split binary image using watershed transformation](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed) +- [Perform 2D spot detection](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d) +- [Perform segmentation using deformable shape models](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/superdsm/ip_superdsm) +- [Switch axis coordinates](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/imagecoordinates_flipaxis/imagecoordinates_flipaxis) +- [Evaluate segmentation](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/visceral_evaluatesegmentation/ip_visceral_evaluatesegmentation) -Works best with -===================== +## Acknowledgment + +This work has been supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI) #031A537C. - * [Docker ParaViewWeb](https://github.com/ThomasWollmann/docker-paraviewweb) - * [Galaxy Imaging](https://github.com/bgruening/docker-galaxy-imaging)