Create a slice object — slice • SMARTR

slice() constructs an S3 object of class 'slice'. A slice object consists of a list of lists storing information about registration, segmentation, raw mapped data and cleaned mapped data. The object attributes are also stored as a list.

Usage

slice(
  slice_ID = NA,
  coordinate = -1,
  atlas_plate = NA,
  conversion_factor = 1.0833,
  bin = 1,
  z_width = 24,
  hemisphere = NULL,
  channels = c("eyfp", "cfos", "colabel"),
  registration_path = "set registration image path",
  segmentation_path = "set segmentation data path",
  slice_directory = NULL,
  left_regions_excluded = c("fiber tracts", "VS"),
  right_regions_excluded = c("fiber tracts", "VS"),
  left_regions_included = NULL,
  right_regions_included = NULL,
  ...
)

Arguments

slice_ID: (str, default = NA) Slice name
coordinate: (num, default = -1) Allen mouse brain atlas coordinate aligning with slice.
atlas_plate: (int, default = NA) Atlas place number. TODO: Currently unused
conversion_factor: (num, 1.0833) pixel-to-micron conversion factor
bin: (int, default = 1) Whether the registration image was binned in ImageJ.
z_width: (num, default = 24) The z-stack width in um.
hemisphere: (str, default = NULL) Hemisphere to process. "left", "right" or NULL is legal.
channels: (str, default = c("cfos", "eyfp", "colabel")) The channels to process.
registration_path: (str, default = 'set registration image path') May deprecate this in favor of slice_directory in future versions.
segmentation_path: (str, default = 'set segmentation image path') Path to image used for segmentation function using base wholebrain::segment() function.
slice_directory: (str, default = NULL) The root directory where slice information such as the registration or segmentation images or txt files are stored for a given slice. TODO: May change the import and registration functions to only rely on this path.
left_regions_excluded: (str, default = ("layer 1","PIR1","TR1","PAA1","NLOT1","OT1","MOBgl","OV","VLPO","SO", "BA","TU","MEAav","ME","TMv","PVp","SUMl","SCzo","fiber tracts","VS")) The list of acronyms corresponding to regions to exclude for this slice's left hemisphere.
right_regions_excluded: (str, default = ("layer 1","PIR1","TR1","PAA1","NLOT1","OT1","MOBgl","OV","VLPO","SO", "BA","TU","MEAav","ME","TMv","PVp","SUMl","SCzo","fiber tracts","VS")) The list of acronyms corresponding to regions to exclude for this slice's right hemisphere.
left_regions_included: (str, default = NULL) List of acronyms of regions to include from left hemisphere. All other regions will be exsluded. If not NULL, takes precedence over left_regions_excluded.
right_regions_included: (str, default = NULL) List of acronyms of regions to include from right hemisphere. All other regions will be exsluded. If not NULL, takes precedence over right_regions_excluded.
...: additional custom keyword pair attributes you'd like to store

Value

A slice, a colloquial term for an object of class 'slice'. A 'slice' object is also a list, with class list.

Details

The slice attributes can be assigned as arguments to the slice constructor function. See the parameters listed for the default values for these attributes Note that you are able to add custom attributes as keyword pairs, if you would like to keep track of an additional piece of information. However, this will only serve a descriptive purpose and will not be used for analysis. You may not need to use all slice attributes but fill out as many are applicable to your experiment.

Examples

slice_example <- slice() # initializes a slice object