a collection of imagej macros I used to (a) stitch and (b) accelerate opening, closing and saving of files for a semi-automated analysis of 2d images of bone histology
quick-stitch.ijm
iterates through all folders in a directory and uses the grid/collection plugin
by Preibisch et al to try and stitch together all tiff images within each folder.
basic-analysis.ijm
lets the user specify
- an input folder which contains the tiff images to analyse
- an (optional) input folder with contains previously stored ROIs
- an output folder
- an input ROI suffix (only zip files whose name ends in this will be used)
- an output ROI suffix
and saves
- the manually drawn rois as zip files ending in output ROI suffix
- the created binary images as tiffs ending in output ROI suffix
- the results of the ImageJ Analyse Particles function as csv files
into the output folder. The scale is hard-coded into the macro, as all my images were taken at the same magnification. Empty selections are ignored, the code just continues to execute. Particles touching the image boundary are not counted.
subtract-two-images-and-analyse-difference.ijm
iterates through user-specified "Minuend" and "Subtrahend" directories and subtracts images in "Subtrahend" from corresponding images in "Minuend" and writes the difference image into a user-specified "Difference" directory. I
mages need to match user-specified suffixes.
Afterwards, the ImageJ Analyse Particles function is run on the difference images and the results are stored as a csv file. Particles touching the image boundary are not counted.
The name is chosen because when I measure secondary osteons on lots of images, I sometimes feel like a stoned wallaby making crop circles in a poppy field.