Posted by
ctrueden on
Mar 16, 2015; 7:41pm
URL: http://imagej.273.s1.nabble.com/Processing-huge-files-tp5012001p5012002.html
Hi Greg,
> this bug seems not to be fixed, as I still get a Java heap memory
> error when trying to do the conversion headless.
Unfortunately, the bug has not yet been uploaded to the ImageJ update site.
More testing and investigation is needed before doing so; it may be a few
more weeks.
For those interested, progress can be followed at:
https://github.com/imagej/imagej-launcher/issues/16> So right now I can open the huge file slice by slice via VirtualStack,
> but I can not write them slice by slice.
Why not? This is supposed to work. What specifically happens if you use
File > Save As > TIFF...? Or Plugins > Bio-Formats > Bio-Formats Exporter?
Regards,
Curtis
On Mon, Mar 16, 2015 at 2:30 PM, Greg <
[hidden email]> wrote:
> Hi,
>
> I want to convert huge .nd2 files (around 60Gb each) to tif, as all
> operations are faster on the tif format.
> The conversion itself is quite painful, as coming from this thread:
>
>
>
http://imagej.1557.x6.nabble.com/Virtual-Memory-in-Headless-Mode-td5011730.html#a5011733>
> this bug seems not to be fixed, as I still get a Java heap memory error
> when
> trying to do the conversion headless. So the conversion needs to be done
> with the Fiji GUI open.
>
> But nevertheless, the problem is the same also with the hopefully soon
> working headless mode: having like 40Gb of virtual memory slows down (any?)
> my PC quite hard. So right now I can open the huge file slice by slice via
> VirtualStack, but I can not write them slice by slice. So that means I
> first
> have to load all sclices into memory (=a Stack) before writing them as
> multi
> page tif to disk.
>
> So my question is, is it somehow possible to append a single slice to a
> disk
> resident file (Virtual Stack) ?
> A workaround might be to write out single tifs for every slice and then
> somehow do the tif concatenation, but I have no idea how exactly this can
> be
> done.
>
> Greets,
> Greg
>
>
>
>
> --
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>
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