API Reference

smlmview(data::AbstractArray{T,N}; kwargs...) -> NamedTuple

Launch an interactive viewer for N-dimensional array data (N ≥ 2).

Arguments

• data: N-dimensional numeric array to display

Keyword Arguments

• display_dims::Tuple{Int,Int}=(1,2): Which dims to display (rowdim, coldim)
• dim_names::Union{Nothing,NTuple{N,String}}=nothing: Optional labels for each dimension
• clip::Tuple{Real,Real}=(0.0, 1.0): Percentile clipping for intensity stretch (0.0, 1.0 = full range)
• title::String="": Window/axis title
• colormap::Symbol=:grays: Colormap for display
• figsize::Tuple{Int,Int}=(800, 700): Maximum figure size in pixels
• show::Bool=true: Whether to display the figure immediately

Returns

NamedTuple with:

• fig: The Makie Figure
• ax: The image Axis
• data: Reference to original array (no copy)
• display_dims: Observable for current display dimensions
• slice_indices: Vector of Observables for each dim's slice index
• colorrange: Observable for intensity range
• cursor_pos: Observable for cursor (row, col) position
• pixel_value: Observable for value under cursor

Keyboard Shortcuts

• 1-9 + 1-9: Two-number sequence sets display_dims (e.g., 21 for transpose)
• c: Cycle colormap (grays, inferno, viridis, turbo, plasma, twilight)
• m: Cycle mapping (linear, log, p199, p595)
• g: Cycle stretch mode (global, slice)
• r: Reset view (fit entire image)
• i/o: Zoom in/out
• e/s/d/f: Pan up/left/down/right
• j/l: Previous/next slice on first slider dim

Example

using SMLMView

# 3D data
data3d = rand(256, 256, 10)
v = smlmview(data3d)

# 4D data with custom display
data4d = rand(64, 64, 10, 5)
v = smlmview(data4d; display_dims=(1, 3), dim_names=("Y", "X", "Z", "T"))

# Change view interactively: press 2 then 3 to show dims (2,3)

Notes

• Data is displayed with standard image orientation: row 1 at top, col 1 at left
• Status bar shows current display dims: (1,2) means dim1→rows, dim2→cols
• For N-dim data, N-2 sliders are created for non-display dimensions

smlmview(channels::Tuple{Vararg{AbstractArray}}; kwargs...) -> NamedTuple

Launch an interactive viewer for multi-channel composite display.

Arguments

• channels: Tuple of 2-3 arrays with matching spatial dimensions

Keyword Arguments

• colors: Channel colors, default CMY (cyan, magenta, yellow)
• names: Channel names for display
• display_dims::Tuple{Int,Int}=(1,2): Which dims are (rows, cols)
• clip::Tuple{Real,Real}=(0.0, 1.0): Percentile clipping (0.0, 1.0 = full range)
• figsize::Tuple{Int,Int}=(800, 700): Max figure size
• show::Bool=true: Whether to display immediately

Keyboard Shortcuts

• 1/2/3: Toggle channel visibility
• m: Cycle mapping (linear, log, percentile)
• g: Cycle stretch mode (global, slice)
• j/l: Previous/next slice
• i/o: Zoom in/out
• r: Reset view

Example

ch1 = rand(256, 256, 10)  # "DAPI"
ch2 = rand(256, 256, 10)  # "GFP"
ch3 = rand(256, 256, 10)  # "Alexa647"
v = smlmview((ch1, ch2, ch3); names=("DAPI", "GFP", "A647"))

configure_display!(; port=8080)

Configure WGLMakie and Bonito server for display. Call once per Julia session. Automatically called on first smlmview() if not already configured.

For VSCode Remote, this sets up the proxy_url for proper WebSocket tunneling.

get_keybindings() -> Dict{String,String}

Return current keybindings as action => key string pairs.

set_keybinding!(action::String, key::String)
set_keybinding!(action::Symbol, key::String)

Set a keybinding for an action. Persists to LocalPreferences.toml.

Example

SMLMView.set_keybinding!(:zoom_in, "k")
SMLMView.set_keybinding!("pan_up", "w")

reset_keybindings!()

Reset all keybindings to defaults. Clears preferences.

list_keys() -> Vector{String}

List all valid key names for keybindings.

list_actions() -> Vector{String}

List all configurable actions.

DEFAULT_CHANNEL_COLORS

Default channel colors for multi-channel composite viewing (Cyan, Magenta, Yellow). CMY additive blending: C+M=Blue, C+Y=Green, M+Y=Red, C+M+Y=White.

CHANNEL_COLOR_PRESETS

Named color presets for multi-channel composite viewing. Available presets: :cmy (default), :rgb, :mgc (Magenta-Green-Cyan).