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Re: [Seg3D] seg3d chrases with +1500 files

Chronological Thread 
  • From: Paul Holcomb <>
  • To: Yeisson Gutiérrez <>,
  • Subject: Re: [Seg3D] seg3d chrases with +1500 files
  • Date: Tue, 31 Jan 2017 13:20:47 +0000


Our lab routinely uses 500GB files and larger in Seg3D with no problems.  Here are two tips for using your files:

1. Convert your files into a tiff stack, rather than loading individual files. Many freely available software options can be used for this, such as ImageJ or Imagemagick.

2. In the bin folder of your Seg3D installation, you will find a "CreateLargeVolume" executable. If applied to your data, it will create a pyramid tiff structure that will allow you to load in extremely large volume data.

If you have any questions on how to implement either of these, please feel free to contact me.

Best wishes,

Paul Holcomb

On Tue, Jan 31, 2017 at 5:26 AM Yeisson Gutiérrez <> wrote:
Dear Mr./Mrs

I've been trying Seg 3D for a few time and I liked so far. However, I'm working with big data sets and that has been an inconvenient. First I though that was because of the size of the files (32 bits TIFF in total 10 - 20 GB), then I compressed the slices and even so the problem continues.... after a while I discovered that was a matter of the number of files and not so much because of the size of these.
Somehow I managed to load about 1300 slices in PNG format  (a single CT scan) but when I want to a apply a filter the program crashes again.
I can tell you that is not a problem of hardware requirements, we have a workstation in my University (University of münster, Germany) with a very good graphic cards (Geforce GTX Titan X) and 512GB of RAM.

Any comment would be greatly appreciated,
Best wishes.

Yeisson Gutiérrez

Institut für Landschaftsökologie
WWU - University of Münster
Heisenbergstr. 2
48149 Münster
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