Contents Menu Expand Light mode Dark mode Auto light/dark, in light mode Auto light/dark, in dark mode Skip to content
omnipose documentation
Logo

Basics

  • Installation
  • GUI
  • Inputs
  • Settings
  • Outputs
  • Training
  • Models

Examples

  • In a notebook
    • The basics in 2D
    • Multiple channels
    • Omnipose in 3D
  • Command line

Project

  • API
    • omnipose.core
      • affinity_to_boundary
      • affinity_to_masks
      • affinity_to_masks2
      • batch_labels
      • boundary_to_affinity
      • boundary_to_masks
      • compute_masks
      • concatenate_labels
      • diameters
      • dist_to_diam
      • div_rescale
      • divergence
      • divergence_torch
      • divergence_torch_old
      • do_warp
      • fill_holes_and_remove_small_masks
      • flow_error
      • follow_flows
      • get_boundary
      • get_contour
      • get_link_matrix
      • get_links
      • get_masks
      • get_masks_cp
      • get_niter
      • labels_to_flows
      • linker_label_to_links
      • links_to_boundary
      • loss
      • masks_to_affinity
      • masks_to_flows
      • masks_to_flows_batch
      • masks_to_flows_torch
      • mode_filter
      • pill_decomposition
      • random_crop_warp
      • random_rotate_and_resize
      • remove_bad_flow_masks
      • scale_to_tenths
      • sigmoid
      • spatial_affinity
      • split_spacetime
      • step_factor
      • steps_batch
      • torch_and
      • torch_and_cpu
      • torch_and_gpu
    • omnipose.utils
      • add_poisson_noise
      • auto_chunked_quantile
      • average_tiles_ND
      • bin_counts
      • border_indices
      • clean_boundary
      • compute_density
      • compute_quantiles
      • correct_illumination
      • cubestats
      • curve_filter
      • extract_skeleton
      • find_boundaries
      • find_files
      • find_nonzero_runs
      • findbetween
      • gamma_normalize
      • generate_slices
      • get_edge_masks
      • get_flip
      • get_module
      • get_neigh_inds
      • get_neighbors
      • get_neighbors_torch
      • get_spruepoints
      • get_steps
      • get_supporting_inds
      • getname
      • hysteresis_threshold
      • is_integer
      • kernel_setup
      • load_nested_list
      • localnormalize
      • localnormalize_GPU
      • make_tiles_ND
      • mask_outline_overlay
      • mono_mask_bd
      • moving_average
      • normalize99
      • normalize99_hist
      • normalize_field
      • normalize_image
      • pnormalize
      • precompute_valid_mask
      • qnorm
      • quantile_rescale
      • ravel_index
      • rescale
      • rotate
      • safe_divide
      • save_nested_list
      • searchsorted
      • skeletonize
      • steps_to_indices
      • subsample_affinity
      • thin_skeleton
      • to_16_bit
      • to_8_bit
      • torch_norm
      • unaugment_tiles_ND
      • unravel_index
    • omnipose.plot
      • apply_ncolor
      • color_from_RGB
      • color_grid
      • color_swatches
      • colored_line
      • colored_line_segments
      • colorize
      • colorize_GPU
      • colorize_dask
      • colorize_dask_fast
      • colorize_dask_matmul
      • create_colormap
      • custom_new_gc
      • faded_segment_resample
      • figure
      • get_aspect
      • image_grid
      • imshow
      • plot_edges
      • rgb_flow
      • segmented_resample
      • set_outline
      • setup
      • split_list
      • truncate_colormap
      • vector_contours
    • cellpose_omni.models
      • BD_MODEL_NAMES
      • C1_BD_MODELS
      • C1_MODELS
      • C2_BD_MODELS
      • C2_MODELS
      • C2_MODEL_NAMES
      • CP_MODELS
      • Cellpose
      • CellposeModel
      • MODEL_DIR
      • MODEL_NAMES
      • MXNET_ENABLED
      • OMNI_INSTALLED
      • SizeModel
      • cache_model_path
      • deprecation_warning_cellprob_dist_threshold
      • model_path
      • models_logger
      • size_model_path
    • cellpose_omni.io
      • adjust_file_path
      • check_dir
      • delete_old_models
      • get_image_files
      • get_label_files
      • getname
      • imread
      • imsave
      • imwrite
      • load_links
      • load_train_test_data
      • logger_setup
      • masks_flows_to_seg
      • outlines_to_text
      • save_masks
      • save_server
      • save_to_png
      • write_links
    • cellpose_omni.plot
      • disk
      • dx_to_circ
      • image_to_rgb
      • interesting_patch
      • mask_overlay
      • mask_rgb
      • outline_view
      • show_segmentation
    • cellpose_omni.metrics
      • aggregated_jaccard_index
      • average_precision
      • boundary_scores
      • flow_error
      • mask_ious
    • cellpose_omni.dynamics
      • compute_masks
      • follow_flows
      • get_masks
      • labels_to_flows
      • map_coordinates
      • masks_to_flows
      • masks_to_flows_cpu
      • masks_to_flows_gpu
      • remove_bad_flow_masks
      • steps2D
      • steps2D_interp
      • steps3D
    • cellpose_omni.transforms
      • average_tiles
      • convert_image
      • make_tiles
      • move_axis
      • move_axis_new
      • move_min_dim
      • normalize99
      • normalize_field
      • normalize_img
      • original_random_rotate_and_resize
      • pad_image_ND
      • random_rotate_and_resize
      • reshape
      • reshape_and_normalize_data
      • reshape_train_test
      • resize_image
      • unaugment_tiles
      • update_axis
  • CLI

More

  • Affinity segmentation
  • Cell contours
  • N-color
  • Cell diameter
  • Gamma
  • Logo
Back to top
Copyright © 2025, Kevin Cutler, University of Washington
Made with Furo