Posted by
ctrueden on
Mar 24, 2015; 2:50pm
URL: http://imagej.273.s1.nabble.com/bfconverter-nd2-to-tif-tp5012133p5012134.html
Hi Greg,
> 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.
Correct. The bfconvert command line tool writes to BigTIFF format, not
ImageJ's "raw" format for large TIFFs. The two are very different. The only
tool that can read the large "raw" TIFFs is ImageJ1. There are currently no
plans for Bio-Formats to support this pseudo-TIFF format.
> 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 ?!
To clarify: I would define a "pure" TIFF as one that is less than 4GB in
size, with 32-bit offsets, according to the official specification. For
files over 4GB, your options are:
A) BigTIFF, which is a "pure" 64-bit TIFF file, and the accepted worldwide
standard; or
B) ImageJ's "raw" TIFF, which not actually a TIFF, but rather raw pixels
preceded by a minimal TIFF header.
> And second also the behaviour (aka lagginess) of Fiji is exactly like
> when working directly on nd2 files.
Can you give more details? Is the delay when first opening the file? And
happens even when "Use virtual stack" is checked? If so, then the problem
is that Bio-Formats parses all TIFF IFDs upfront, which can incur a
significant delay for large files with many planes. There are certainly
things that can be done on the Bio-Formats side to improve the performance
there; I suggest starting a discussion on the ome-users mailing list [1].
Regards,
Curtis
[1]
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/On Tue, Mar 24, 2015 at 9:02 AM, Greg <
[hidden email]> wrote:
> 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
>
>
>
>
>
> --
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>
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