morphoviewer

Usage

import React from "react"
import { MorphologyCanvas } from "@bbp/morphoviewer"

export default functon MyCellViewer({ swc }: { swc: string }) {
    const refPainter = React.useRef(new MorphologyCanvas())
    React.useEffect(
        () => {
            refPainter.current.swc = swc
        },
        [swc]
    )
    return <canvas ref={(canvas) => refPainter.canvas = canvas} />
}

Utils

colorContrast(background: string, ...colors: string[]): string

Returns the element from colors that has the better contrast with background.

This can be handy if you need to overlay text on the canvas.

The alpha will be ignored for background, but not for colors.

AtlasPainter

const painter = new AtlasPainter()

MorphologyPainter

const painter = new MorphologyPainter()

painter.colors

Define the colors of the background and the different sections of the cell in CSS style.

painter.colors.soma = "#ef558a"
painter.colors.apicalDendrite = "rgb(32, 88, 150)"

painter.eventColorsChange

This event is dispatched anytime a color is changed by setting any attribute of painter.colors.

painter.eventMouseWheelWithoutCtrl

The mouse wheel is used to zoom in/out. But if the viewer is embeded in a long page, this behavior can prevent the page from scrolling and frustrate the user.

That's why, if the viewer is not in fullscreen mode, the zoom will only work if the user holds Control key while mouse wheeling. This event is dispatched if an attempt to use the mouse wheel without holding Control is detected in non fullscreen mode.

painter.minRadius

When dendrites are very long and very thin, they can start to disappear. That's why the painter has a minimal radius for them to keep them always visible.

Default value is 1 pixel.

painter.toggleFullscreen()

Toggle the associated canvas in fullscreen mode.

painter.resetCamera()

The camera will target the soma and the zoom will be set as to see the whole cell. It will face the Z axis of the morphology, with the Y axis looking to the top.

painter.pixelScale (readonly)

Returns the space size of a screen pixel. This can be used to compute a scale bar.

See painter.eventPixelScaleChange.

painter.eventPixelScaleChange

This event is dispatched every time painter.pixelScale changes.

painter.computeScalebar(options)

Input:

options: Partial<{
    preferedSizeInPixels: number
    units: Record<string, number>
    values: number[]
}>

• preferedSizeInPixels: The scalebar's size we target. Depending on the constaints, the scalebar actual size can be different. Default to 240 pixels.
• units: The units we are allowd to use and their scale against the default space unit. Default to { nm: 1e-3, µm: 1, mm: 1e3, m: 1e6, km: 1e9 }.
• values: The rounded values we are allowed to use. This will prevent the scalebar from displaying something like 27.1542 mm. Default to [1, 2, 5, 10, 20, 25, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900].

Output:

{
    sizeInPixel: number
    value: number
    unit: string
}

• sizeInPixel: Actual size of the scalebar computed for the resulting value and unit.
• value: Numerical value to display.
• unit: Unit of expression of value.

painter.colorBy

A string enum that defines how the cell must be colored.

• "section": Use painter.colors to color the soma, axon ans dendrites.
• "distance": Use a gradient (green, yello, red) to show the distance from the soma. Red is the farest point from the soma.

painter.radiusType

A float between 0 and 1 to know how to interpret radius information from the SWC file.

• 0: Variable radius (default).
• 1: Constant radius.

In real life, dendrites tend to be thicker near to the soma and become thiner at the end. Trees in the woods behave like this too.

Setting 0 will give you the real radius. And the 1 will set the same radius everywhere (a constant one that is the average of all the values).

If needed, to temper the effect, you can set any value between 0 and 1 to get an interpolation.

painter.canvas

The canvas onto display the 3D cell.

painter.swc

The string content of a SWC file that describes the tree structure of the current cell.