Method Zoo

Visual gallery of all built-in pattern methods. Each card shows an example raw image alongside the illumination pattern the method would generate with the parameters listed. Gallery images are rendered automatically at docs build time from sample images in documentation/zoo_sources/.

Stimulation / Pattern Methods

Inner fraction

$Inner fraction$

Applies a bar to the center of the long axis

TOML key: "embryo_inner" · API: InnerPatternMethod

Parameters used in this example:

Parameter	Value
`fraction_length`	`0.1`

Outer fraction

$Outer fraction$

Applies a bar to the poles of the long axis

TOML key: "embryo_outer" · API: OuterPatternMethod

Parameters used in this example:

Parameter	Value
`fraction_length`	`0.1`

Moving Bar

Moving Bar

Periodic bar sweeping along the y-axis at constant speed.

API: BarPattern

Parameters used in this example:

Parameter	Value
`duty_cycle`	`0.2`
`bar_speed`	`1.0`
`period`	`100`

Rotating Bar

Rotating Bar

Spoke-like bars rotating around the center of the field.

TOML key: "rotate_bar" · API: RotatingBarPattern

Parameters used in this example:

Parameter	Value
`num_bars`	`12`
`angular_velocity`	`2.0`
`bar_width`	`20`

Generic Nucleus Control

Generic Nucleus Control

Subclass this method to apply per-cell intensity

API: NucleusControlMethod

Bang-Bang Controller

Bang-Bang Controller

Applies light if nucleus is below target intensity

TOML key: "binary_nucleus_clamp" · API: BinaryNucleusClampModel

Parameters used in this example:

Parameter	Value
`clamp_target`	`75`

Open loop intensity cycle

Open loop intensity cycle

Applies light for a given period with a 50% duty cycle

TOML key: "global_cycle" · API: GlobalCycleModel

Rotate CCW

Rotate CCW

Illuminates the half of each cell pointing counter-clockwise around the field center.

TOML key: "rotate_ccw" · API: RotateCcwModel

Parameters used in this example:

Parameter	Value
`channel`	`'seg_channel'`

Move Out

Move Out

Illuminates the outward-facing half of each cell.

TOML key: "move_out" · API: MoveOutModel

Parameters used in this example:

Parameter	Value
`channel`	`'seg_channel'`

Move In

Move In

Illuminates the inward-facing half of each cell.

TOML key: "move_in" · API: MoveInModel

Parameters used in this example:

Parameter	Value
`channel`	`'seg_channel'`

Radial Wave

Radial Wave

Concentric rings propagating outward from the center.

API: WavePattern

Parameters used in this example:

Parameter	Value
`duty_cycle`	`0.2`
`wave_speed`	`10`
`period`	`100`
`direction`	`1`

Circle

Circle

Filled circle centerd on the camera field of view.

TOML key: "circle" · API: CirclePattern

Parameters used in this example:

Parameter	Value
`rad`	`60`

Full On

Full On

Illuminates the entire camera field of view.

TOML key: "full_on" · API: FullOnPattern

Adding a new method to the gallery — attach a zoo_meta class variable to your PatternMethod subclass (see src/pyclm/core/patterns/zoo.py for the ZooMeta dataclass) and add the corresponding source image to documentation/zoo_sources/<source>.tif. A <source>_seg.tif label image is optional; synthetic blobs are used when absent.