How to load hdf5 images from a macro

Use the command "Scriptable load HDF5...", for example:

run("Scriptable load HDF5...", "load=" + "[D:\\MRI\\Sylvain\\MuVI SPIM\\Stack_0_Channel_0\\Cam_Left_00000.h5] datasetnames=/Data nframes=1 nchannels=1");

How to save the selections from the roi-manager with the image stack

If you only want to show which parts have been selected on each slice, you can use "flatten" from the roi-manager and then save the stack as a tif-image. Things are a bit more complicated if you want to save the selections with the stack in a way that you can get them back as selections after reopening the stack. To achieve this you can create an overlay from the roi-manager via the command Image>Overlay>FromROIManager. Then save the stack. After reopening the stack you can get the selections back via Image>Overlay>ToROIManager.