import_segmentation (generic function) — import_segmentation

Custom method for importing segmentation data for a slice object. This is a flexible method for importing channels aside from cfos and eyfp that use the same ImageJ segmentation macros common to the Denny Lab. Other labs may use this method. This method works best when following saving segmentation data with the same naming conventions using the 3D Roi Manager within the 3D ImageJ Suite. Segmentation data is saved in two'.txt' files which output the results of the Measure 3D and Quantif 3D options of the 3D Roi Manager plugin,respectively. A description of what each of those these options measure is provided in the online documentation.

The naming conventions for the ".txt" file storing the Quantif3D results are Q_*_{channel}_*_{channel}.txt, where the * indicates a wildcard character(s) and channel is the channel name without brackets. E.g. "Q_G_eYFP_258_1_1_eYFP.txt"

The naming conventions for the ".txt" file storing the Measure 3D are M_*_{channel}_*.txt where the * indicates a wildcard character(s) and channel is the channel name without brackets. E.g "M_G_eYFP_258_1_1.txt".

The wildcards characters may be used to store things like date or slice naming information.

The locations of these files must be specified in the slice_directory attribute of the slice_object. Otherwise, the root folder containing the registration image is searched. This attribute can be stored when initializing the slice object or can be edited afterwards.

Method for custom importation of segmentation data for a mouse object

Usage

import_segmentation_custom(x, ...)

# S3 method for slice
import_segmentation_custom(
  s,
  channel,
  x_col = NULL,
  y_col = NULL,
  meas_path = NULL,
  quant_path = NULL
)

# S3 method for mouse
import_segmentation_custom(
  m,
  channel,
  slice_ID = NA,
  hemisphere = NULL,
  x_col = NULL,
  y_col = NULL,
  meas_path = NULL,
  quant_path = NULL
)

Arguments

...
s: slice object
channel: (str) channel to import
x_col: = NULL,
y_col: = NULL,
meas_path: = NULL,
quant_path: = NULL
m: mouse object
slice_ID: (str) ID of slice
hemisphere: (str)'left', 'right' or NULL

Value

s slice object

m mouse object

Examples

s <-  import_segmentation_custom(s, mouse_ID = "255", channel = "cfos")
#> Error in import_segmentation_custom(s, mouse_ID = "255", channel = "cfos"): object 's' not found
m <-  import_segmentation(m, slice_ID = "1_10", channels = c("PV"), replace = FALSE)
#> Error in import_segmentation(m, slice_ID = "1_10", channels = c("PV"),     replace = FALSE): could not find function "import_segmentation"