Glossary

Glossary#

frame#: A single 2D raster scan of the field of view, saved as one TIFF page with shape (height, width). The fundamental unit of acquired image data.
slice#: One z-position in a volumetric acquisition. May contain multiple frames if framesPerSlice > 1.
volume#: One complete z-stack containing all slices. Represents a single 3D snapshot of the sample.
timepoint#: One volume acquisition in a time series. For 2D acquisitions, equivalent to one frame.
piezo#: A piezoelectric actuator used to rapidly move the objective or sample stage along the z-axis. Enables fast volumetric imaging by sequentially stepping through z-positions. In ScanImage, controlled via si.hStackManager parameters.
framesPerSlice#: ScanImage parameter (si.hStackManager.framesPerSlice) specifying how many 2D frames are acquired at each z-position before moving to the next slice. When > 1, enables optional frame averaging for improved SNR.
logAverageFactor#: ScanImage parameter (si.hStackManager.logAverageFactor) controlling hardware-level frame averaging. When > 1, frames are averaged during acquisition rather than saved individually.
de-interleave#: The process of reorganizing raw LBM data from z-interleaved format (z1t1, z2t1, z3t1, z1t2…) to plane-sequential format (z1t1, z1t2, z1t3, z2t1…) for compatibility with downstream processing pipelines.
multipage_tiff#: A TIFF file containing multiple 2D images (pages) stored sequentially. Standard format for ScanImage acquisitions where each frame is saved as a separate page.
region-of-interest#: A set of 1 or more 2D planes which are stitched together to form the full image.
num_pixel_xy#: The number of pixels [X, Y] in each region-of-interest.
roi_width_px#: The size of the region-of-interest on its shortest dimension.
roi_height_px#: The size of the region-of-interest on its longest dimension.
Field-of-view#: The total size (um) of the raw stitched image with no trimming operations.
image-length#: The number of pixels on the long axis of the raw .tiff file.
image-width#: The number of pixels on the short, slow-galvo axis of the raw .tiff file.
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).