# Glossary

**Acquisition frame**

One recorded observation in a time series. This workshop labels frames `0` through `29`. A frame index is not elapsed time unless the acquisition interval is known.

**Additive blending**

A display mode that adds light from image layers, helping two channels appear together. Bright overlap can saturate, so inspect each channel separately too.

**Array**

A rectangular collection of numbers. A microscopy image is represented as an array whose axes may describe time, depth, rows, and columns.

**Channel**

An image series acquired for a particular signal. The source layer names here are DNA and mitochondria; a layer name alone does not establish the identity of a tracked particle.

**Colormap**

A rule that maps numerical intensity to displayed color. Changing it does not alter stored intensity values.

**Contrast limits**

The low and high intensity values mapped to the dark and bright ends of a layer’s display. Values outside the limits may appear clipped.

**Detection**

A supplied candidate location at one frame. A displayed point does not prove biological identity or tracking correctness.

**Downsampling factor**

How much the original spatial grid is reduced. Factor 4 keeps roughly every fourth-scale spatial dimension using the preparation method. It reduces workload but loses fine detail. It does not change the 30-frame time axis.

**Dtype**

The number format stored by an array. `uint16` stores non-negative integers from 0 through 65,535.

**Environment (`.venv`)**

The folder containing this workshop’s Python and packages. `uv sync --locked` creates it. It stays inside the workshop folder and does not need manual activation.

**Gamma**

A nonlinear display adjustment that redistributes apparent brightness between the contrast limits. It changes appearance, not the source values.

**Intensity**

A numeric image value measured at a voxel. Brightness on screen also depends on contrast, gamma, colormap, opacity, and blending.

**Jupyter kernel**

The Python process that runs notebook cells. Choose **Python (napari workshop)** so the notebook uses the workshop environment.

**Layer**

One image, points table, tracks table, or other object in the napari viewer. Each layer has its own visibility and display controls.

**Lazy loading**

A strategy that delays reading array chunks until needed. It can reduce RAM use, but it does not shorten the initial download, guarantee instant interaction, or remove GPU limits.

**Maximum-intensity projection (MIP)**

A 2D image containing the brightest voxel found along a chosen axis, often depth. It shows bright structures together but discards their positions along the projected axis.

**Napari**

An interactive desktop viewer for multidimensional images and related data. It opens separately from the JupyterLab browser.

**Notebook cell**

A block of Markdown explanation or Python code. Run code cells from top to bottom with **Shift+Enter**.

**Opacity**

How transparent a layer appears. Reducing opacity can reveal another layer beneath it.

**Playback fps**

Frames shown per second in an exported movie. It controls viewing speed and does not establish acquisition timing.

**Point**

A marker displayed at a coordinate. In this workshop points visualize precomputed detection-table rows.

**Projection**

A lower-dimensional summary of an array. Always state which axis and operation were used because a projection loses information.

**Scale**

The conversion between array steps and physical units. Calibration is not yet confirmed for this dataset, so course coordinates remain in source voxels and no physical scale bar is claimed.

**Slice**

One plane selected from a volume. Unlike a projection, it does not combine all depth planes.

**Source voxel**

One element of the original three-dimensional image grid. Tables retain source-voxel coordinates even when the prepared image array is spatially reduced; the course loader aligns them.

**Track**

An inferred association of positions across frames, identified by `id`. It is a model result that may contain errors or ambiguities, not a newly measured image channel.

**Track tail**

The recent portion of a track displayed behind its current point. Tail length describes a window in frame indices, not a particle count.

**Voxel**

A volume element: the 3D counterpart of a pixel. Its physical size must come from verified calibration.

**Zero-based indexing**

Counting that starts at zero. Thirty frames therefore use indices `0` through `29`.