diff --git a/README.md b/README.md index 433cc311..bb10e4af 100644 --- a/README.md +++ b/README.md @@ -13,45 +13,46 @@ If Galaxy Image Analysis helped with the analysis of your data, please do not fo ## 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) +- [Compute image features](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/mahotas_features/ip_mahotas_features) +- [Compute image segmentation and object detection performance measures](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/segmetrics/ip_segmetrics) +- [Concatenate images or channels](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/concat_channels/ip_concat_channels) - [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) +- [Convert image format](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage) +- [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) +- [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) - [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) +- [Evaluate segmentation](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/visceral_evaluatesegmentation/ip_visceral_evaluatesegmentation) +- [Extract 2D features](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction) - [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) +- [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) +- [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 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 color decomposition](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/ip_color_deconvolution) +- [Perform curve fitting](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/curve_fitting/ip_curve_fitting) +- [Perform histogram equalization](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization) +- [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) - [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) +- [Perform segmentation using region-based fitting of overlapping ellipses](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/rfove/rfove/2023.11.12+galaxy0) +- [Perform segmentation using deformable shape models](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/superdsm/ip_superdsm) - [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) +- [Permutate image axes](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/permutate_axis/ip_permutate_axis) - [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) +- [Show image info](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo) - [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) +- [Split label map using morphological operators](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/split_labelmap/ip_split_labelmap) - [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) +- [Threshold image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold) +- [Visualize detections](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/detection_viz/ip_detection_viz) ## Acknowledgment