Glossary

Glossary#

skewness #: How often do you get an outlier in the pixel activity across time, good for calcium indicators because theyre flat relative to a few events over the course of a recording.
mean_img#: The average of the registered movie over time. Used as a baseline representation of the structural signal.
max_proj#: The maximum value per pixel over time. Highlights regions with high fluorescence, useful for detecting active areas.
meanImgE#: Enhanced mean image generated by Suite2p using filtering and sharpening operations. Useful for anatomical segmentation when available.
anatomical segmentation#: ROI detection based solely on static images (e.g. mean or max projection), ignoring fluorescence time dynamics.
functional segmentation#: ROI detection based on pixelwise correlations across time, identifying spatially contiguous regions with similar activity patterns.
seed#: A pixel or region in the image used as the starting point for growing a potential ROI. Seeding is based on high-intensity regions in the filtered image, and forms the initial guess for the shape and location of a neuron.
Delta F over F0#: \(\Delta F / F_0\) (Delta F over F naught) refers to the fractional change in fluorescence relative to a baseline signal F₀. This is a common normalization used in calcium imaging and neural activity recordings.
segmentation#: The general process of dividing an image based on the contents of that image, in our case, based on neuron location.
source-extraction#: Umbrella term for all of the individual processes that produce a segmented image.
deconvolution#: The process performed after segmentation to the resulting traces to infer spike times from flourescence values.
Rigid-registration#: The object retains shape and size.
Non-rigid-registration#: The object is moved and transforms shape or size.
pixel-resolution#: The length of each pixel, in micron (px/um).
LBM#: Light Beads Microscopy. A volumetric imaging technique where z-planes are acquired as ScanImage channels using multiple beamlets.
piezo#: Piezo z-stack acquisition. Uses a piezo actuator to step through z-positions, acquiring frames at each depth before moving.
LBMPiezo#: Combined LBM and piezo acquisition. Has both LBM characteristics (>2 channels as beamlets) and piezo stepping. Used for pollen calibration workflows.
OutputMetadata#: A class that computes adjusted metadata when writing subsets of data. Automatically scales z-step when selecting every Nth plane, and invalidates frame rate for non-contiguous frame selections.
OME-NGFF#: Open Microscopy Environment Next Generation File Format. A specification for storing multidimensional imaging data in Zarr format with standardized metadata for coordinate transforms and axis definitions.
volumetric output#: Writing 4D data (T, Z, Y, X) to a single file with plane/frame selection support. Both TIFF (ImageJ hyperstack) and Zarr (OME-NGFF v0.5) formats are supported.
reactive metadata#: Metadata that automatically adjusts based on data selection. For example, dz doubles when selecting every 2nd z-plane, and fs becomes invalid for non-contiguous frame selections.