bfconverter nd2 to tif

Posted by Greg on Mar 24, 2015; 2:02pm
URL: http://imagej.273.s1.nabble.com/bfconverter-nd2-to-tif-tp5012133.html

Hi,

I am trying to convert (huge) nd2 files to the ImageJ native tif(f?) format. I am using the Bio-Formats commandline tool bfconvert (http://www.openmicroscopy.org/site/support/bio-formats5.0/users/comlinetools/conversion.html), which behaves very nice with respect to memory usage.

I tried both

bfconvert -bigtiff input.nd2 output.tif

and

bfconvert -bigtiff input.nd2 output.tiff

but I do not think that the outputs are in a native ImageJ format. First, when I open one of the produced output files in Fiji, the Bio-Formats Input Option Dialog opens, which should not be the case when having a 'pure' tif, right ?! And second also the behaviour (aka lagginess) of Fiji is exactly like when working directly on nd2 files.

An additional problem is, that the output is no hyperstack anymore, but that I can fix later..

So how do I convert nd2 files to 'native tif ImageJ' on the commandline ?

Greets,
Greg