autoims
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autoims
vandeplaslab/autoims-docs
Home
Getting started
Tasks
Tasks
Glossary
Metadata
Reference project
Contact
Contact
Contact information
Pre-processing
Pre-processing
Convert raw data (single-dataset)
Tags and names (single-dataset)
Mass alignment (single-dataset)
Ion mobility alignment (single-dataset)
Register GeoJSON masks from QuPath (single-dataset)
Register image2image HDF5 masks (single-dataset)
Create merged project based on tags (merged-dataset)
Create merged project from select single-datasets (merged-dataset)
Create subset project from single-datasets (subset-project)
Normalization (single-dataset)
Normalization (multi-dataset)
Normalization (merged-project)
Average ion mobility heatmap (single-dataset)
Average mass spectrum (single-dataset)
Skyline mass spectrum (single-dataset)
Average ion mobility heatmap / mask (single-dataset)
Average mass spectrum / mask (single-dataset)
Skyline mass spectrum / mask (single-dataset)
Mass calibration (single-dataset)
Features
Features
M/z feature detection (multi-dataset)
M/z feature detection (subset-project)
M/z feature detection (single-dataset)
Ion mobility feature detection (single-dataset)
Extract ion centroids (single/multi-dataset)
Extract ion centroids (subset-project)
Filter ion centroids (single-dataset)
Filter ion centroids (multi-dataset)
Annotation
Annotation
Annotate average mass spectrum (merged-project)
Annotate mass spectra (single-dataset)
Annotate mass spectrum (multi-dataset)
Annotate average mass spectrum (merged-project)
Annotate mass spectrum (subset-project)
Machine Learning
Machine Learning
Unsupervised training (single-dataset)
Unsupervised training (merged-project)
Average mass spectrum / cluster (single-dataset)
XGBoost training (single-dataset)
XGBoost training (merged-project)
Supervised training (single-dataset)
Supervised training (merged-project)
Average mass spectrum / class (single-dataset)
Statistics
Statistics
Group statistics of ion centroids (multi-dataset)
Group statistics of mass spectra (multi-dataset)
Distributions of ion centroids (single-dataset)
Distributions of ion centroids (multi-dataset)
Quality Control
Quality Control
Compute quality control metrics (multi-dataset)
Visualise quality control metrics (multi-dataset)
Visualise quality control metrics (subset-project)
Visualization
Visualization
Compare peaks (interactive, multi-dataset)
Compare spectra (interactive, multi-dataset)
Compare mosaic images (single-dataset)
Compare mosaic images (multi-dataset)
Compare spectra (one-vs-one; multi-dataset)
Compare spectra (one-vs-one; single-dataset)
Export
Export
Dataset to imzML (single-dataset)
Export mass spectrum (single-dataset)
Export ion centroids (single-dataset)
Specialized Workflows
Specialized Workflows
Create ratio images (single-dataset)
Process PASEF-MS1 imaging data (single-dataset)
Process PASEF-MS2 imaging data (single-dataset)
Examples
Examples
Multi-dataset
PASEF
Requests/Bug reports
Changelog
Multi-dataset
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