Setting animation gallery¶

spaCR includes short, deterministic GIFs for settings whose effect is easier to understand visually. In the desktop interface, hovering a setting shows its explanation; pressing the teal Animation word in that tooltip’s footer reveals the corresponding animation to the right of the text. It is revealed for that setting only — the next setting is text again until its own Animation is pressed, and nothing is decoded until it is. Set Setting animations in Preferences to show them without asking.

The diagrams use a shared biological grammar: white fibroblast or motile immune-cell outlines, blue nuclei with unequal nucleoli, teal Toxoplasma tachyzoites inside an outline-only parasitophorous vacuole, and soft-magenta Golgi cisternae. Filled regions are translucent and the rounded field perimeter remains white on black.

The cell, nucleus and nucleoli, two-parasite vacuole, and Golgi use the reviewed, artist-authored SVG paths checked into tools/. Qt renders those exact Bezier paths at high resolution before each animation frame is composited, keeping the outlines smooth at small sizes. Source-template SHA-256 hashes are recorded in the manifest.

Animations are resolved by exact setting key through spacr.setting_animations; the assets and manifest are generated reproducibly by tools/generate_setting_animations.py.

Mask filtering¶

Cell — Remove border objects¶

Settings: cell_remove_border_objects, remove_border_cells

Cell — Minimum object area¶

Settings: cell_min_area, cell_min_size

Cell — Maximum object area¶

Settings: cell_max_area

Cell — Minimum intensity percentile¶

Settings: cell_min_intensity_percentile

Cell — Maximum intensity percentile¶

Settings: cell_max_intensity_percentile

Nucleus — Remove border objects¶

Settings: nucleus_remove_border_objects, remove_border_nuclei

Nucleus — Minimum object area¶

Settings: nucleus_min_area, nucleus_min_size

Nucleus — Maximum object area¶

Settings: nucleus_max_area

Nucleus — Minimum intensity percentile¶

Settings: nucleus_min_intensity_percentile

Nucleus — Maximum intensity percentile¶

Settings: nucleus_max_intensity_percentile

Pathogen — Remove border objects¶

Settings: pathogen_remove_border_objects, remove_border_pathogens

Pathogen — Minimum object area¶

Settings: pathogen_min_area, pathogen_min_size

Pathogen — Maximum object area¶

Settings: pathogen_max_area

Pathogen — Minimum intensity percentile¶

Settings: pathogen_min_intensity_percentile

Pathogen — Maximum intensity percentile¶

Settings: pathogen_max_intensity_percentile

Organelle — Remove border objects¶

Settings: organelle_remove_border_objects, organelle_remove_border, remove_border_organelles

Organelle — Minimum object area¶

Settings: organelle_min_area, organelle_min_size

Organelle — Maximum object area¶

Settings: organelle_max_area, organelle_max_size

Organelle — Minimum intensity percentile¶

Settings: organelle_min_intensity_percentile

Organelle — Maximum intensity percentile¶

Settings: organelle_max_intensity_percentile

Mask repair¶

Merge edge-pathogen cells¶

Settings: merge_edge_pathogen_cells

Adjust fragmented cells¶

Settings: adjust_cells

Cell perimeter merge¶

Settings: cell_perimeter_fraction

Cell intensity merge¶

Settings: cell_intensity_merge, cell_intensity_threshold_method, cell_intensity_percentile

Cell watershed split¶

Settings: cell_intensity_split, cell_area_multiplier, cell_min_distance, cell_min_object_area

Nucleus perimeter merge¶

Settings: nucleus_perimeter_fraction

Nucleus intensity merge¶

Settings: nucleus_intensity_merge, nucleus_intensity_threshold_method, nucleus_intensity_percentile

Nucleus watershed split¶

Settings: nucleus_intensity_split, nucleus_area_multiplier, nucleus_min_distance, nucleus_min_object_area

Pathogen perimeter merge¶

Settings: pathogen_perimeter_fraction

Pathogen intensity merge¶

Settings: pathogen_intensity_merge, pathogen_intensity_threshold_method, pathogen_intensity_percentile

Pathogen watershed split¶

Settings: pathogen_intensity_split, pathogen_area_multiplier, pathogen_min_distance, pathogen_min_object_area

Organelle perimeter merge¶

Settings: organelle_perimeter_fraction

Organelle intensity merge¶

Settings: organelle_intensity_merge, organelle_intensity_threshold_method, organelle_intensity_percentile

Organelle watershed split¶

Settings: organelle_intensity_split, organelle_area_multiplier, organelle_min_distance, organelle_min_object_area

Fill holes in masks¶

Settings: fill_in

Segmentation¶

Cell probability threshold¶

Settings: cell_CP_prob

Cell flow threshold¶

Settings: cell_FT

Cell diameter¶

Settings: cell_diameter

Nucleus probability threshold¶

Settings: nucleus_CP_prob

Nucleus flow threshold¶

Settings: nucleus_FT

Nucleus diameter¶

Settings: nucleus_diameter

Pathogen probability threshold¶

Settings: pathogen_CP_prob

Pathogen flow threshold¶

Settings: pathogen_FT

Pathogen diameter¶

Settings: pathogen_diameter

Organelle diameter¶

Settings: organelle_diameter

Organelle probability threshold¶

Settings: organelle_CP_prob

Organelle flow threshold¶

Settings: organelle_FT

Image preprocessing¶

Cell background subtraction¶

Settings: remove_background_cell, cell_background

Cell signal-to-noise¶

Settings: cell_Signal_to_noise

Nucleus background subtraction¶

Settings: remove_background_nucleus, nucleus_background

Nucleus signal-to-noise¶

Settings: nucleus_Signal_to_noise

Pathogen background subtraction¶

Settings: remove_background_pathogen, pathogen_background

Pathogen signal-to-noise¶

Settings: pathogen_Signal_to_noise

Image normalization percentiles¶

Settings: normalization_percentiles, normalize, normalize_plots

Organelle preprocessing¶

Fill small organelle holes¶

Settings: organelle_fill_holes

Split touching organelle spots¶

Settings: organelle_watershed_spots

Skeletonize organelle networks¶

Settings: organelle_skeletonize

Rolling-ball background correction¶

Settings: organelle_rolling_ball, organelle_rolling_ball_radius

Organelle local contrast (CLAHE)¶

Settings: organelle_clahe, organelle_clahe_clip_limit

Mask organelles within cells¶

Settings: organelle_mask_within_cells

Organelle segmentation threshold¶

Settings: organelle_log_threshold, organelle_unet_threshold

Plot appearance¶

Mask outline thickness¶

Settings: outline_thickness

Crop output¶

Keep bounding-box context¶

Settings: use_bounding_box

Dilate crop masks¶

Settings: dialate_pngs, dialate_png_ratios

Choose crop target¶

Settings: crop_mode

Crop canvas size¶

Settings: png_size

Measurement¶

Derive cytoplasm compartment¶

Settings: cytoplasm

Radial-distance shells¶

Settings: radial_dist, distance_gaussian_sigma

Keep or remove uninfected cells¶

Settings: uninfected

Tracking & volumetric¶

Remove transient tracks¶

Settings: timelapse_remove_transient, timelapse_frame_limits

Maximum linking displacement¶

Settings: timelapse_displacement, ultrack_max_distance, t_max_displacement_px, t_max_displacement_um

Tracking memory¶

Settings: timelapse_memory

Timepoint overlap threshold¶

Settings: t_link_threshold

Z-plane stitch threshold¶

Settings: stitch_threshold

Z projection¶

Settings: z_projection, all_to_mip, pick_slice

Project volumes for tracking¶

Settings: t_project_for_tracking

Remove overly straight tracks¶

Settings: straightness_filter, straightness_threshold

Smooth per-track outliers¶

Settings: zscore_thresh

Cell-division linking¶

Settings: ultrack_division_weight

Contour smoothing¶

Settings: ultrack_contour_sigma

Image UMAP¶

UMAP neighborhood size¶

Settings: n_neighbors

UMAP minimum distance¶

Settings: min_dist

Show object images¶

Settings: plot_images

Remove image canvas¶

Settings: remove_image_canvas

Show cluster outlines¶

Settings: plot_outlines

Show embedding points¶

Settings: plot_points

Smooth cluster outlines¶

Settings: smooth_lines

Remove cluster noise¶

Settings: remove_cluster_noise

Sample images by cluster¶

Settings: plot_by_cluster

Embedding point size¶

Settings: dot_size

Embedding image zoom¶

Settings: img_zoom

Density clustering radius¶

Settings: eps, min_samples, clustering

Alignment & stitching¶

Tile overlap¶

Settings: overlap

Tile seam blending¶

Settings: blend