Puzzled with Nucleus Counter and the flex-file and its opener

[Md Tamjidul Hoque]

Dear All

        I was extending the  "Nucleus Counter" (under "Plugins >
Particle Analysis > ...")  for some particular application.

       Problem 1: I do not see "Nucleus Counter" is performing the same
for same image with same options selected
                        for version WCIF_ImageJ
(http://www.uhnresearch.ca/facilities/wcif/imagej/) and version
MBF_ImageJ (http://www.macbiophotonics.ca/imagej/)
                        ... why is that?
                       It seems working as desired with WCIF_ImageJ and
not with MBF_ImageJ but I am relying on MBF_ImageJ to open .flex file
(http://www.loci.wisc.edu/bio-formats-format/evotecperkinelmer-opera-flex)
only.
                       ... why is that?
     
      Problem 2: How can I use WCIF_ImageJ to open .flex file? [Can I
borrow something from MBF_ImageJ into WCIF_ImageJ]

      Problem 3: If a .flex file have many pages - it shows stack size
'0' (for the following code, but do count correctly if you open
differently: By ImageJ and then capture the Image window rather than
from file ),
                       whereas if I convert it in tiff and check the
tiff instead  it shows the number of pages correctly.

                                                        ImagePlus imp =
new ImagePlus(my_file_names.get(i));
                                                        ImageStack stack
= imp.getStack();
                                                        //imp.show();
     
     Problem 4:    Even if I block "imp.show();" - flex files are shown
on the screen but the tiff/tif files are not shown.


Any help is much appreciated.
Thanks
Tamjid