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opendvp

  • API Reference
    • Input / Output
      • opendvp.io.adata_to_qupath
      • opendvp.io.adata_to_voronoi
      • opendvp.io.import_thresholds
      • opendvp.io.quant_to_adata
      • opendvp.io.segmask_to_qupath
      • opendvp.io.DIANN_to_adata
      • opendvp.io.import_perseus
      • opendvp.io.export_adata
      • opendvp.io.export_figure
    • Metrics
      • opendvp.metrics.coefficient_of_variation
      • opendvp.metrics.nan_difference
    • Plotting
      • opendvp.plotting.plot_graph_network
      • opendvp.plotting.stacked_barplot
      • opendvp.plotting.abundance_histograms
      • opendvp.plotting.correlation_heatmap
      • opendvp.plotting.coefficient_of_variation
      • opendvp.plotting.density
      • opendvp.plotting.dual_axis_boxplots
      • opendvp.plotting.imputation_qc
      • opendvp.plotting.pca_loadings
      • opendvp.plotting.rankplot
      • opendvp.plotting.upset
      • opendvp.plotting.volcano
    • Preprocessing
      • opendvp.pp.impute_marker_with_annotation
    • Tools
      • opendvp.tl.filter_by_abs_value
      • opendvp.tl.filter_by_annotation
      • opendvp.tl.filter_by_ratio
      • opendvp.tl.filter_features_byNaNs
      • opendvp.tl.impute_gaussian
      • opendvp.tl.spatial_autocorrelation
      • opendvp.tl.spatial_hyperparameter_search
      • opendvp.tl.stats_anova
      • opendvp.tl.stats_average_samples
      • opendvp.tl.stats_bootstrap
      • opendvp.tl.stats_ttest
    • Utils
      • opendvp.utils.parse_color_for_qupath
    • Imaging
      • opendvp.imaging.mask_to_polygons
  • Tutorials
    • T1: Image single-cell analysis
    • T2: Downstream Proteomics
    • T3: Proteomics Integration
  • openDVP the framework
    • Experimental
      • Imaging
      • Tissue and Slides
    • Computational
      • Install opendvp
      • Getting started with MCMICRO
      • Getting started with SOPA
  • Contribution Guide
  • .md

Computational

Contents

  • Introductory tutorials
  • Image processing pipelines
    • Get started with MCMICRO
    • Get started wih SOPA
    • Other image processing approaches

Computational#

Introductory tutorials#

  • Get started with uv for python management

Image processing pipelines#

Get started with MCMICRO#

  • Get started with using MCMICRO

Get started wih SOPA#

  • Get started with using SOPA

Other image processing approaches#

  • scPortrait

  • Harpy

previous

Tissue and Slides

next

Install opendvp

Contents
  • Introductory tutorials
  • Image processing pipelines
    • Get started with MCMICRO
    • Get started wih SOPA
    • Other image processing approaches

By Jose Nimo