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_feature_extraction
• 2d_filter_segmentation_by_features
• 2d_histogram_equalization
• 2d_simple_filter
• 2d_split_binaryimage_by_watershed
• 3d_tensor_feature_dimension_reduction
• anisotropic_diffusion
• auto_threshold
• bfconvert
• binary2labelimage
• binaryimage2points
• color_deconvolution
• concat_channels
• coordinates_of_roi
• count_objects
• curl_post
• curve_fitting
• detection_viz
• image_info
• image_registration_affine
• imagecoordinates_flipaxis
• labelimage2points
• landmark_registration
• mahotas_features
• mergeneighboursinlabelimage
• overlay_images
• permutate_axis
• points_association_nn
• points2binaryimage
• points2labelimage
• projective_transformation
• projective_transformation_points
• scale_image
• segmetrics
• slice_image
• split_labelmap
• spot_detection
• superdsm
• unzip
• visceral_evaluatesegmentation
• 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

• pugixml

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

usegalaxy.eu

• Galaxy Image Analysis tools