Dear image.sc community,
I have a problem opening 6D datasets of a beating zebrafish heart from the Leica Digital Light Sheet microscope in FIJI.
With 6D I mean, XY, C, T, Z, L (loop). I can save as tiff file series, lif or lof files.
The desired outcome is to obtain small “.ome.tiff-files” of XYCT for each Z-plane and each Loop.
I created a macro-based workflow with a work around, using tiff files series. That works for basically all my datasets.
The problem is that it takes forever at the microscope to save big datasets with 750.000 individual tiff-files. It can take a whole weekend and more. To transfer these files afterwards to a server or harddrive takes another day. Similar problems occur when converting the files in the Leica Software from lif to tiff. I could solve the problem by reducing the hyperstack by one dimension directly at the microscope (by splitting Z-planes for example). Unfortunately the Leica-software does not allow this.
I need to save as .lif or .lof from the microscope and ideally load parts of the datasets in ImageJ. When I use Bioformats “Specify subset” the order of the imagestack is a mess. Of course there is no XYCTZL stack order. I spent a long time, trying to recognize a pattern that I can use macros to bring order into the chaos, but the channels, frames and Z-planes are jumping without an obvious sense.
I would be very happy for any solution, suggestion or idea.
Thanks a lot in advance.