Glossary

Ashlar: A Python library for stitching microscopy images with subpixel precision.
Best Focus: The plane in a Z-stack that has the highest focus quality according to a focus metric.
Channel: A specific wavelength or color channel in a microscopy image, often corresponding to a specific fluorophore or stain.
Composite Image: An image created by combining multiple channels, often with different weights.
Focus Metric: A mathematical measure of image focus quality, such as normalized variance, Laplacian energy, or Tenengrad variance.
Grid Size: The number of tiles in the x and y directions in a microscopy acquisition.
ImageXpress: A high-content screening platform from Molecular Devices that generates microscopy images with a specific file naming convention.
Max Projection: A method of combining a Z-stack by taking the maximum intensity value at each pixel position across all planes.
Mean Projection: A method of combining a Z-stack by taking the average intensity value at each pixel position across all planes.
Metadata: Information about the microscopy acquisition, such as pixel size, grid dimensions, and acquisition settings.
Microscope Handler: A component in EZStitcher that handles microscope-specific functionality, such as filename parsing and metadata extraction.
Opera Phenix: A high-content screening platform from PerkinElmer that generates microscopy images with a specific file naming convention.
Pixel Size: The physical size of a pixel in the microscopy image, typically measured in micrometers.
Plate: A container for samples in high-content screening, typically with multiple wells arranged in a grid.
Position Generation: The process of determining the relative positions of tiles for stitching.
Preprocessing: Image processing operations applied to individual tiles before stitching, such as background subtraction or histogram equalization.
Reference Channel: The channel used for position generation in stitching.
Site: A specific field of view or tile in a microscopy acquisition.
Stitching: The process of combining multiple overlapping images into a single larger image.
Subpixel Precision: Alignment of images with precision finer than a single pixel, achieved through interpolation.
Tile: A single image in a grid of images that will be stitched together.
Tile Overlap: The percentage of overlap between adjacent tiles in a microscopy acquisition.
Well: A specific location in a plate where a sample is placed, typically identified by a letter-number combination (e.g., A01).
Z-Index: The index or position of a plane in a Z-stack.
Z-Stack: A series of images taken at different focal planes along the z-axis, capturing 3D information about a sample.