stitchGiottoLargeImage | R Documentation |
Function to stitch together multiple field of view (FOV) images into a
single final image. Images are loaded into Giotto as giottoLargeImage
and
stitched based on a set of FOV positions into a single final giottoLargeImage
.
stitchGiottoLargeImage(
largeImage_list = NULL,
gobject_list = NULL,
largeImage_nameList = NULL,
FOV_positions = NULL,
FOV_xcol = NULL,
FOV_ycol = NULL,
FOV_inverty = FALSE,
method = c("mosaic", "merge"),
round_positions = FALSE,
filename = NULL,
dataType = NULL,
fileType = NULL,
dryRun = TRUE,
overwrite = FALSE,
verbose = TRUE
)
largeImage_list |
list of |
gobject_list |
list of |
largeImage_nameList |
list of names of |
FOV_positions |
dataframe of FOV positions. Values (if any) are directly added to current image mapping |
FOV_xcol |
column name for FOV position x values |
FOV_ycol |
column name for FOV position y values |
FOV_inverty |
make FOV y position values negative |
method |
method of stitching images (mosaic: average overlapping area values, merge:values get priority by order of images given) |
round_positions |
[boolean] round image positions. May be necessary to run. |
filename |
file name to write the stitched image to. Defaults to |
dataType |
(optional) values for |
fileType |
(optional) image format (e.g. .tif) If not given, defaults to format given in the filename |
dryRun |
[boolean] plot placeholder bounding rectangles where FOV images will be stitched without actually proceeding with the full image stitching and saving process. |
overwrite |
[boolean] overwrite if filename to save image as already exists. Defaults to TRUE |
verbose |
[boolean] be verbose |
This function is time consuming. Setting a save location through the
filename
parameter is also highly recommended as file size will likely be large.
This function creates a single stitched image from multiple FOV tiles and saves that
image to disk as it works. When finished, the pointer to that new image is loaded in
as a giottoLargeImage
object.
Note: Dry runs are on by default and dryRun
param must be set to FALSE
to proceed with the final stitching operation.
largeGiottoImage
object with pointer to stitched image
To ensure that disk space and time is not wasted, this function defaults to previewing the stitching operation.
The final image is stitched together from multiple FOV tiles. The FOV_positions
parameter accepts a table of x and y values for where each FOV tile should be placed
when performing the stitch. Which columns are the x and y values are determined by
the FOV_xcol
and FOV_ycol
params respectively. FOV tiles are at full resolution
with a starting position where either the lower left or upper left of the image touch the origin
depending on the value of FOV_inverty
param. The FOV image is then translated according
to the x and y shift values.
Many imaging systems may treat the origin according to image convention where (0,0) is at the
upper left of an image. This is at odds with coordinate convention and what Giotto uses internally
where the coordinate (0,0) is at the lower left. The FOV_inverty
defaults to FALSE, but if
set to TRUE, then FOV tile images will start with the upper left touching (0,0) and all y values
given through FOV_positions
and FOV_ycol
will be treated as negative y shift values.
There are multiple datatypes defining the range of intensity values that images can be saved
with. Setting a value with the dataType
para is optional and Giotto attempts
to determine compatible data type to save the image as automatically.
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