Cropping several parts of a set of images from multiple folders

Posted by otills on
URL: http://imagej.273.s1.nabble.com/Cropping-several-parts-of-a-set-of-images-from-multiple-folders-tp3689264.html

Hi, I'm fairly new to Image J so I apologise if this is a trivial question.

I'm using the plugin MicroManager to capture sequences from various positions on a multi-well tray repeatedly i.e. a looped command. Each time point is given a folder in which the images from each location are stored in subfolders (labelled with their position). Each position is imaging four wells from the multi-well trays and I'm only interested in the very centre of each well. Therefore what I want to do is find a way of cropping each set of images (stack) into four separate images. In addition to this I'd also like to be able combine the images from the same location at different time points into a single stack .. I have been doing this using the concatenate function, however is there a way of doing this as a batch?

Is there an easy way of doing this?

I've found the batch process folder macro http://rsb.info.nih.gov/ij/macros/BatchProcessFolders.txt which seems ideal as it will enable me to run the command at a higher level than individual sub-folders, however I don't know how to incorporate cropping into this macro and, if this is the most feasible way of achieving this, labelling the separate images in a way that enables me to identify which well each stack of images corresponds to.

Many thanks,

Oli Tills