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* adds code of conduct Adds code of conduct from galaxyproject/tools-iuc repo. * adds matrix badge * adds DOI badge * changes matrix badge color * adds list of tools * adds contribution instructions * fixes link in README.md * updates CONTRIBUTING.md * updates README.md * fixes some issues * updates PR template * removes versions from tool list in README.md
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| Code of Conduct | ||
| =============== | ||
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| 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: | ||
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| https://galaxyproject.org/community/coc/ |
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| # Contributing | ||
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| 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. | ||
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| ## How to Contribute | ||
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| * 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. |
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| [](https://travis-ci.org/BMCV/galaxy-image-analysis) | ||
| [](https://doi.org/10.1016/j.jbiotec.2017.07.019) | ||
| [](https://matrix.to/#/#galaxyproject_imaging:matrix.org) | ||
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| Galaxy Image Analysis | ||
| ======================== | ||
| # Galaxy Image Analysis | ||
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| 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). | ||
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| 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). | ||
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| 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: <https://doi.org/10.1016/j.jbiotec.2017.07.019> | ||
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| 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 | ||
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| - [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) | ||
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| Works best with | ||
| ===================== | ||
| ## Acknowledgment | ||
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| 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. | ||
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| * [Docker ParaViewWeb](https://github.com/ThomasWollmann/docker-paraviewweb) | ||
| * [Galaxy Imaging](https://github.com/bgruening/docker-galaxy-imaging) |