Glossary

Glossary#

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).