Posted by
ctrueden on
Mar 19, 2015; 7:19pm
URL: http://imagej.273.s1.nabble.com/Processing-huge-files-tp5012001p5012070.html
Hi Greg,
> what I want is to write as Stack out slice by slice to one big file.
A couple of suggestions to try.
Firstly, have you tried the "bfconvert" command line tool [1]?
It would allow you to convert your ND2 files to (Big-)TIFF without needing
ImageJ at all. It supports BigTIFF via the "-bigtiff" flag.
Secondly, you can use the Bio-Formats API to write out the data plane by
plane [2] to a single large file (TIFF or otherwise). You would need to
write Java code, or use a non-macro scripting language that can access Java
API (e.g., Jython or Groovy) [3].
Regards,
Curtis
P.S. Some day ImageJ2 will be far enough along that the paradigm will
shift: "opening" the data will always be virtual, with ImageJ not needing
to read all planes in advance; processing the data will page planes in and
out of RAM as needed transparently; and saving/export will work as usual,
with very little RAM overhead since it is also done fully plane-by-plane.
We are getting close, but not quite there yet...
[1]
http://openmicroscopy.org/site/support/bio-formats/users/comlinetools/conversion.html[2]
http://openmicroscopy.org/site/support/bio-formats/developers/export.html[3]
http://imagej.net/ScriptingOn Wed, Mar 18, 2015 at 5:25 AM, Greg <
[hidden email]> wrote:
> Hi Curtis,
>
> thx for your answer and sorry for my delay. So of course writing out slice
> by slice works, if I write every slice as a new file. But what I want is to
> write as Stack out slice by slice to one big file. So in principle to save
> RAM I want to do the following:
>
> open one slice from Virtual Stack
>
> do some processing
>
> Append that slice to a disk resident Stack.
>
> So that only one slice has to be in memory at a time, but in the end I have
> a processed disk resident copy of the huge input Virtual Stack.
>
> Best,
> Greg
>
>
>
>
>
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