CODEWITHSUNDEEP
rimageimagej
Lillian
Lillian

Reputation: 31

How to load XY coordinates of binary outline saved as tiff file?

I'm using the R package Momocs to compare outlines of shapes I've traced in ImageJ and saved as binary image tiffs. For example: one outline of snail teeth. Momocs requires a matrix of X and Y coordinates, and I'm having trouble converting from image to coordinates.

On the one hand: ImageJ has an option to Save As... XY Coordinates, but this only works on a selection. I can use the wand tool to select the outline, but it encircles the one-pixel-wide outlines, e.g. a straight line would have coordinates of a long rectangle, describing both sides of the line. This makes me see my snail teeth in double-vision (image example of one tooth close-up) and may adversely affect analysis.

On the other hand: Momocs has an import_jpg1 command, but when I convert my images to jpegs (or make jpegs from scratch), they end up with light-colored pixels as noise around the outlines. I tried the packages tiff and rtiff, but their outputs are not XY coordinates of the black parts of the tiff, and I'm not familiar enough with the outputs to understand how I might convert them to XY coordinates.

Can anyone help me do one (or multiple!) of these things:

Thanks in advance for any help!

Upvotes: 1

Views: 727

Answers (1)

aoles
aoles

Reputation: 1545

You can easily extract the matrix of XY coordinates of pixels meeting certain criteria with R's function which by specifying arr.ind=TRUE. To illustrate this approach I use the Bioconductor package EBImage to directly load the sample PNG file from the provided URL. readImage is a wrapper for the functions provided in R packages jpeg, png and tiff, so apart from PNGs it also opens JPEG and TIFF files.

### Install EBImage
# source("https://bioconductor.org/biocLite.R")
# biocLite("EBImage")

img <- EBImage::readImage("https://i.sstatic.net/ZFTxu.png")

mat <- which(img==0, arr.ind=TRUE, useNames=FALSE)
head(mat)

##      [,1] [,2]
## [1,]  121   53
## [2,]  120   54
## [3,]  118   55
## [4,]  119   55
## [5,]  117   56
## [6,]  116   57

EBImage offers a wide range of tools for working with image data in R which might be of interest to you, such as functions for manipulating, filtering and displaying images. See the package vignette for an overview.

Upvotes: 1

Related Questions