Biomedical Computer Vision (BMCV)
Prof. Dr. Karl Rohr
Galaxy Image Analysis
The BMCV Group is developing workflows and tools for web-based analysis of microscopy image data and systematic phenotyping of human cells. We developed Galaxy Image Analysis as extension of the Galaxy platform to address the requirements of microscopy image analysis. Workflows and tools for automated extraction of cellular phenotypes are integrated and deployed by Bioconda. Selected workflows are integrated within ELIXIR services like Galaxy Europe. Tools and workflows are also provided under GitHub. We use Galaxy Image Analysis in different interdisciplinary cooperations. The work is carried out within HD-HuB of the de.NBI project. Below is a list our contributions.
Galaxy Tools (Examples)
- 2d_auto_local_threshold
- 2d_auto_threshold
- 2d_feature_extraction
- 2d_filter_segmentation_by_features
- 2d_histogram_equalization
- 2d_simple_filter
- 3d_tensor_feature_dimension_reduction
- anisotropic_diffusion
- background_removal
- bfconvert
- binary2labelimage
- binaryimage2points
- bioformats2raw
- colocalization_viz
- color_deconvolution
- colorize_labels
- concat_channels
- coordinates_of_roi
- count_objects
- crop_image
- curl_post
- curve_fitting
- detection_viz
- image_info
- image_math
- image_registration_affine
- imagecoordinates_flipaxis
- label_to_binary
- labelimage2points
- landmark_registration
- landmark_registration_ls
- mahotas_features
- mergeneighboursinlabelimage
- morphological_operations
- orientationpy
- overlay_images
- overlay_moving_and_fixed_image
- overlay_segmentation_mask
- permutate_axis
- plantseg
- points2binaryimage
- points2labelimage
- points_association_nn
- projective_transformation
- projective_transformation_points
- repeat_channels
- rfove
- scale_image
- segmetrics
- slice_image
- split_image
- split_labelmap
- spot_detection_2d
- superdsm
- unzip
- visceral_evaluatesegmentation
- voronoi_tessellation
- wsi_extract_top_view
Workflows (Examples)
- RNAi screen analysis
- Capturing mitoflashes
- MALDI & HE co-registration
- Registration of images based on landmarks
- Registration of images based on intensity information
- Spot tracking
- Segmentation
Galaxy Interactive Environments
- Paraview-based N-dimensional image viewer
- Openslide-based WSI viewer
Bioconda Packages
- DCMTK
- Visceral-EvaluateSegmentation
- Openslide
- VNL
- gdk-pixbuf
- paraview
- itk
- deepmedic
- munkres
- pymot
- zeroc-ice
- python-omero
- xcftools
- medpy
- bftools
- segmetrics
- SuperDSM
Conda Forge Packages
Galaxy
- Image datatypes support
- Polygon datatypes support
- Several bugfixes (e.g., UI, scheduling, core)
Galaxy Docker
- Several bugfixes
Galaxy Docker Imaging Flavour
- Recipe maintenance
- Tool selection
Galaxy Jupyter GIE
- Several bugfixes
Galaxy Ansible
- Several bugfixes
Bioblend
- Several bugfixes
Galaxy Training Network
- Tutorial on basics in Galaxy Image Analysis
- Tutorial on RNAi screen analysis