README.md

In ornelles/EBImageExtra: Helper Functions for EBImage

Description

This is a collection of functions to extend the EBImage package and provide helper functions for processing micrographs. These functions require the EBImage package and are typically used with the virustiter package. The virustiter package requires the lattice and latticeExtra packages.

Functional Groups

Extensions to EBImage

• circularity - more precisely calculate the circularity of an image object
• perimeter - more precisely calculate the perimeter of an image object
• ni - a vectorized wrapper to the normalize() function with defaults for 12-bit images
• bresenham - Bresenham's integer line "plotting" algorithm
• pnpoly - determine if points are within a polygon (algorithm of W. Randolph Franklin)

Image stacks

• stackObjects2 - place detected objects with the bounding box in an image stack
• interleave - reorganize an image stack by interleaving the images
• plotStack - plot an image stack with optional labels
• locatorStack - interact with a plotted image stack to select frames
• labelStack - label frames of a plotted image stack

Filters

• sobel - the Sobel filter for edge detection
• usm - the Unsharp mask filter to sharpen images by increasing local contrast
• hpf - the High pass filter to exclude slowly varying signals

Region of interest management

EBImage uses the S4 Image class to store and process images. A region of interest is an Image object with the additional class named Roi and a slot named loc to store the original x,y and x2,y2 location of the rectangular region of interest. This class of objects allows the image and original location to be passed in one object.

• getROI - get a region of interest
• putROI - put a region of interest (with scaling) at one of nine locations in an image
• drawROI - draw a frame around or within an image to highlight the region of interest
• as.Roi - convert Image object to Roi object or reset the loc slot of an Roi object to the image dimensions

Micrograph utilities

• scaleBar - add horizontal scale bar to image
• crop - crop a grayscale or binary image to exclude zero pixels at the edges
• boxtext - add text with a shaded background box to a plot
• dp - wrapper to call dev.print for the current device window where the global logical variable SaveImage can be used to determine whether a file will be saved or not
• inset - function to be added...maybe... add a framed inset to an image by sequential use of getROI, drawROI, and putROI to select a region from an image, draw a frame about the selected region and then place the selection as a framed inset

At the moment, inset can be emulated by something like the following:

  plot(img) # assuming 'img' holds an Image object
  ins <- getROI(img)
  ans <- drawROI(img, ins, lwd = 2)
  ans <- putROI(ans, ins, "topright", lwd = 4)
  plot(ans)

License

GPL-3

ornelles/EBImageExtra documentation built on Aug. 10, 2022, 11:44 p.m.