_config.yml

title: "Bioimage Analysis Training Resources"
email: "image-analysis-support@embl.de"
description: > # this means to ignore newlines until "baseurl:"
  A collection of material for teaching image analysis.
  Includes concept maps, exercises, example data
contributing: CONTRIBUTING

baseurl: "/training-resources" # this should be the name of your repository
url: "https://neubias.github.io" # this should be the base hostname & protocol for your site

# Build settings
# Turn on built-in syntax highlighting.
highlighter: rouge
exclude: ["README.md", "TEACHING.md"]

# options are: "NONE", "ImageJ GUI", "ImageJ Macro", "Jython", "MATLAB"
default-platform: "NONE"

life_cycle: "stable"
kind: "lesson"

module_order:
- tool_installation
- pixels
- lut
- multichannel_images
- spatial_calibration
- multidimensional_image_basics
- datatypes
- image_file_formats
- big_image_file_formats
- ome_tiff
- ome_zarr
- table_file_formats
- image_inspection_and_presentation
- correlative_image_rendering
- volume_slicing
- projections
- volume_viewer
- segmentation
- binarization
- auto_threshold
- connected_components
- measure_shapes
- workflow_segment_2d_nuclei_measure_shape
- image_formation_fluo_mic
- measure_intensities
- global_background_correction
- filter_neighbourhood
- median_filter
- workflow_segment_2d_noisy_nuclei_filter_objects_measure_shape
- filter_morphological
- local_background_correction
- filter_objects
- distance_transform
- watershed
- workflow_nuclei_and_cells_segmentation
- skeletonization
- similarity_transforms
- script_run
- coding_with_llms
- script_record
- script_variables
- string_concat
- output_saving
- script_functions
- script_for_loop
- batch_processing
- batch_qc_and_exploration
- fetching_user_input
- script_env
- deep_learning_run_segmentation
- manual_segmentation
- workflow_golgi_per_cell

# Sites
repository: <USERNAME>/<PROJECT>
cc_by_human: "https://creativecommons.org/licenses/by/4.0/"


# Specify that things in the episodes collection should be output.
collections:
  modules:
    output: true
    permalink: /:path/index.html
  extras:
    output: true
    permalink: /:path/index.html

# Set the default layout for things in the modules collection.
defaults:
  - values:
      root: .
      layout: page
  - scope:
      path: ""
      type: modules
    values:
      root: ..
      layout: module
  - scope:
      path: ""
      type: extras
    values:
      root: ..
      layout: page

# Files and directories that are not to be copied.
exclude:
  - Makefile
  - bin/
  - .Rproj.user/
  - .vendor/
  - vendor/
  - .docker-vendor/