Fixing a macro.

I fixed an ImageJ macro "4D_PE_Processor" . I wrote this sometime ago, probably in 2004 summer to process 4D sequences of Medaka fish embryo. Since those files were really huge (Gbytes!) data set, batch procesing script was something necessary. It batch processes projections, resizing and contrast enhance ment for the tiff-file series generated by perkin-Elmer UltraView software. There was a e-mail from a friend in Weizmann Institute in Israel that the macro does not read his image sequence. The problem was rather simple: file naming. Since the frame number and z-slice number information could be known only in the file name, if the file name has something wrong, then the macro does not recognize the file properly.

A problem about Perkin-Elmer Tiff files are that it has two types of file naming. In old software, file naming is

prefix_****_***.tif (* are digits)

and the new one is like

prefix_T****_(channel wavelength)_Z***.tif.

the first four digits indicate time points and the latter three digits indicate Z slice position. I made the macro so that it reads time point by the order of underscore ("_"). Then if one uses underscore in the prefix, the detection of timepoints and z-slices will be totally messed up. As a work round, I changed the macro to recognize "_0" rather than "_" alone. It needs more improvement since the macro does not work if timepoint is more than 999 or if z-slices are greater than 99.