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mkdocs.yml
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site_name: autoims
site_url: https://github.com/vandeplaslab/autoims-docs
site_author: Lukasz Migas
site_description: >-
Suite of tools for image registration and visualisation.
# Repository
repo_name: vandeplaslab/autoims-docs
repo_url: https://github.com/vandeplaslab/autoims-docs
# Copyright
copyright: Copyright © 2023 - present Van de Plas lab
extra_css:
- assets/css/extra.css
theme:
name: material
logo: assets/icon.svg
favicon: assets/icon.svg
palette:
- scheme: default
primary: red
accent: red
toggle:
icon: material/weather-night
name: Switch to dark mode
- scheme: slate
primary: red
accent: red
toggle:
icon: material/weather-sunny
name: Switch to light mode
features:
- navigation.instant
- navigation.top
- navigation.tabs
- navigation.expand
- search.highlight
- search.suggest
- toc.integrate
- toc.follow
markdown_extensions:
- admonition
- pymdownx.details
- pymdownx.superfences
- changelog
- attr_list
- md_in_html
- pymdownx.keys
- tables
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- def_list
- pymdownx.tasklist:
custom_checkbox: true
plugins:
- search
- autorefs
- minify:
minify_html: true
- glightbox
- offline
- exclude:
glob:
- _templates/*
nav:
- Home: index.md
- Getting started: getting_started.md
- Tasks:
- Glossary: extras/glossary.md
- Metadata: extras/metadata.md
- Reference project: extras/reference-project.md
- Contact:
- Contact information: tasks/user.md
- Pre-processing:
- Convert raw data (single-dataset): tasks/pre_convert.md
- Tags and names (single-dataset): tasks/pre_rename.md
- Mass alignment (single-dataset): tasks/pre_mz_align.md
- Ion mobility alignment (single-dataset): tasks/pre_im_align.md
- Register GeoJSON masks from QuPath (single-dataset): tasks/pre_geojson_registration.md
- Register image2image HDF5 masks (single-dataset): tasks/pre_image2image_registration.md
- Create merged project based on tags (merged-dataset): tasks/pre_merge_datasets.md
- Create merged project from select single-datasets (merged-dataset): tasks/pre_merge_subset_datasets.md
- Create subset project from single-datasets (subset-project): tasks/pre_subset_datasets.md
- Normalization (single-dataset): tasks/pre_normalization_single.md
- Normalization (multi-dataset): tasks/pre_normalization_multi.md
- Normalization (merged-project): tasks/pre_normalization_project.md
- Average ion mobility heatmap (single-dataset): tasks/pre_average_heatmap.md
- Average mass spectrum (single-dataset): tasks/pre_average_spectrum.md
- Skyline mass spectrum (single-dataset): tasks/pre_skyline_spectrum.md
- Average ion mobility heatmap / mask (single-dataset): tasks/wf_mask_heatmap_single.md
- Average mass spectrum / mask (single-dataset): tasks/wf_mask_spectrum_single.md
- Skyline mass spectrum / mask (single-dataset): tasks/wf_mask_skyline_spectrum_single.md
- Mass calibration (single-dataset): tasks/pre_mz_calibrate.md
- Features:
- M/z feature detection (multi-dataset): tasks/wf_mz_detect_multi.md
- M/z feature detection (subset-project): tasks/wf_mz_detect_subset.md
- M/z feature detection (single-dataset): tasks/wf_mz_detect_single.md
- Ion mobility feature detection (single-dataset): tasks/wf_im_detect_single.md
- Extract ion centroids (single/multi-dataset): tasks/wf_mz_extract_centroids.md
- Extract ion centroids (subset-project): tasks/wf_mz_extract_centroids_subset.md
- Filter ion centroids (single-dataset): tasks/wf_mz_filter_single_centroids.md
- Filter ion centroids (multi-dataset): tasks/wf_mz_filter_multi_centroids.md
- Annotation:
- Annotate average mass spectrum (merged-project): tasks/wf_mz_annotate_project.md
- Annotate mass spectra (single-dataset): tasks/wf_mz_annotate_single.md
- Annotate mass spectrum (multi-dataset): tasks/wf_mz_annotate_multi.md
- Annotate average mass spectrum (merged-project): tasks/wf_mz_annotate_project.md
- Annotate mass spectrum (subset-project): tasks/wf_mz_annotate_subset.md
- Machine Learning:
- Unsupervised training (single-dataset): tasks/wf_unsupervised_single.md
- Unsupervised training (merged-project): tasks/wf_unsupervised_project.md
- Average mass spectrum / cluster (single-dataset): tasks/wf_unsupervised_spectrum_single.md
- XGBoost training (single-dataset): tasks/wf_xgboost_single.md
- XGBoost training (merged-project): tasks/wf_xgboost_project.md
- Supervised training (single-dataset): tasks/wf_supervised_single.md
- Supervised training (merged-project): tasks/wf_supervised_project.md
- Average mass spectrum / class (single-dataset): tasks/wf_supervised_spectrum_single.md
- Statistics:
- Group statistics of ion centroids (multi-dataset): tasks/wf_centroids_ion_statistics.md
- Group statistics of mass spectra (multi-dataset): tasks/wf_mz_ion_statistics.md
- Distributions of ion centroids (single-dataset): tasks/wf_compare_single_distribution.md
- Distributions of ion centroids (multi-dataset): tasks/wf_compare_multi_distribution.md
- Quality Control:
- Compute quality control metrics (multi-dataset): tasks/wf_qc_compute.md
- Visualise quality control metrics (multi-dataset): tasks/wf_qc_visualise_multi.md
- Visualise quality control metrics (subset-project): tasks/wf_qc_visualise_subset.md
- Visualization:
- Compare peaks (interactive, multi-dataset): tasks/wf_compare_mz_peaks.md
- Compare spectra (interactive, multi-dataset): tasks/wf_compare_mz_spectra_interactive.md
- Compare mosaic images (single-dataset): tasks/wf_compare_single_mosaic.md
- Compare mosaic images (multi-dataset): tasks/wf_compare_mosaic.md
- Compare spectra (one-vs-one; multi-dataset): tasks/wf_compare_mz_spectra_grid.md
- Compare spectra (one-vs-one; single-dataset): tasks/wf_compare_mz_spectra_single_grid.md
- Export:
- Dataset to imzML (single-dataset): tasks/ex_export_imzml.md
- Export mass spectrum (single-dataset): tasks/ex_mass_spectrum.md
- Export ion centroids (single-dataset): tasks/ex_centroids.md
- Specialized Workflows:
- Create ratio images (single-dataset): tasks/wf_compare_single_ratio.md
- Process PASEF-MS1 imaging data (single-dataset): tasks/wf_pasef_ms1.md
- Process PASEF-MS2 imaging data (single-dataset): tasks/wf_pasef_ms2.md
- Examples:
- Multi-dataset: examples/multi-dataset.md
- PASEF: examples/pasef.md
- Requests/Bug reports: request.md
- Changelog: changelog.md