help > V3D can read >2G TIF/LSM stacks now!
Showing 1-8 of 8 posts
Aug 18, 2010 10:08 PM | Hanchuan Peng
V3D can read >2G TIF/LSM stacks now!
Due to the limitation of libtiff, V3D once could only read >2G
image stacks only in two ways: (1) use V3D's Raw format, and (2)
Use the "Importing image series" function in the main menu. A third
way sometimes also worked, i.e. using an existing V3D Bioformat_IO
plugin or ITK_IO plugin to read data.
But it would be really nice if TIFF / LSM stacks that are larger than 2G can be directly loaded in V3D, without using the plugins, or the RAW format!
** Now, V3D v2.515 can read > 2G large TIFF/LSM files! **
The building script for Mac was also updated and tested, for both 64 and 32 bit systems.
There are still some minor problems, however. But I am going to fine-tune the system based on users' feedback!
-hanchuan
But it would be really nice if TIFF / LSM stacks that are larger than 2G can be directly loaded in V3D, without using the plugins, or the RAW format!
** Now, V3D v2.515 can read > 2G large TIFF/LSM files! **
The building script for Mac was also updated and tested, for both 64 and 32 bit systems.
There are still some minor problems, however. But I am going to fine-tune the system based on users' feedback!
-hanchuan
Aug 19, 2010 02:08 AM | Hanchuan Peng
RE: V3D can read >2G TIF/LSM stacks now!
Tests on three Linux machines (redhat and ubuntu 9.1 64bit, and
10.4 32bit) are all sucecssful.
Just run "sh ./build.linux" to build the application.
Tests on Mac Pro 10.5 (Leopard) both 32bit and 64 bit, 10.6 (Snow Leopard) 64bit are all successful.
Ihor/Aurelien, - Now it's a GO!
I will find time to build the Windows versions.
-hanchuan
Originally posted by Hanchuan Peng:
Just run "sh ./build.linux" to build the application.
Tests on Mac Pro 10.5 (Leopard) both 32bit and 64 bit, 10.6 (Snow Leopard) 64bit are all successful.
Ihor/Aurelien, - Now it's a GO!
I will find time to build the Windows versions.
-hanchuan
Originally posted by Hanchuan Peng:
Due to the limitation of libtiff, V3D once could
only read >2G image stacks only in two ways: (1) use V3D's Raw
format, and (2) Use the "Importing image series" function in the
main menu. A third way sometimes also worked, i.e. using an
existing V3D Bioformat_IO plugin or ITK_IO plugin to read data.
But it would be really nice if TIFF / LSM stacks that are larger than 2G can be directly loaded in V3D, without using the plugins, or the RAW format!
** Now, V3D v2.515 can read > 2G large TIFF/LSM files! **
The building script for Mac was also updated and tested, for both 64 and 32 bit systems.
There are still some minor problems, however. But I am going to fine-tune the system based on users' feedback!
-hanchuan
[/userquote]
But it would be really nice if TIFF / LSM stacks that are larger than 2G can be directly loaded in V3D, without using the plugins, or the RAW format!
** Now, V3D v2.515 can read > 2G large TIFF/LSM files! **
The building script for Mac was also updated and tested, for both 64 and 32 bit systems.
There are still some minor problems, however. But I am going to fine-tune the system based on users' feedback!
-hanchuan
[/userquote]
Aug 19, 2010 10:08 AM | Ihor Smal
RE: V3D can read >2G TIF/LSM stacks now!
I managed to build new v3d without any problems for ubuntu 10.4
64bit and mac os x 10.5 32bit, still have to test on os x 10.6 (32
and 64).
Aug 20, 2010 02:08 PM | Hanchuan Peng
RE: V3D can read >2G TIF/LSM stacks now!
I have just tested on both Linux and Mac that V3D can open 7.83GB
and 5.13GB 3-color LSM-format image stacks, without a problem!
Thanks for Tanya for the testing data.
Thanks for Tanya for the testing data.
Sep 4, 2010 10:09 PM | Hanchuan Peng
RE: V3D can read >2G TIF/LSM stacks now!
As of now (v2.525), I added an option for a user to determine
whether or not use Mylib or Libtiff to load tiff/lsm files. Libtiff
reading engine will be faster but is subject to data type and file
size (<2G) limitation. Mylib is slower, may have some unexpected
behaviors but cannot load big TIF/LSM files (as mentioned in
previous post, we tested on 8G single image stack w/o a problem).
MyLib, btw, may load some TIf files as 16bit but libtiff may reads it as 8bit. The display won't have a problem, except the data would be scaled differently by different readers.
MyLib, btw, may load some TIf files as 16bit but libtiff may reads it as 8bit. The display won't have a problem, except the data would be scaled differently by different readers.
Sep 8, 2010 10:09 PM | Hanchuan Peng
RE: V3D can read >2G TIF/LSM stacks now!
a typo! -- mylib can load BIG tiff files! :-)
Originally posted by Hanchuan Peng:
Originally posted by Hanchuan Peng:
As of now (v2.525), I added an option for a user
to determine whether or not use Mylib or Libtiff to load tiff/lsm
files. Libtiff reading engine will be faster but is subject to data
type and file size (<2G) limitation. Mylib is slower, may have
some unexpected behaviors but cannot load big TIF/LSM files (as
mentioned in previous post, we tested on 8G single image stack w/o
a problem).
MyLib, btw, may load some TIf files as 16bit but libtiff may reads it as 8bit. The display won't have a problem, except the data would be scaled differently by different readers.[/userquote]
MyLib, btw, may load some TIf files as 16bit but libtiff may reads it as 8bit. The display won't have a problem, except the data would be scaled differently by different readers.[/userquote]
Mar 28, 2017 12:03 PM | marionac
RE: V3D can read >2G TIF/LSM stacks now!
I am currently working with Vaa3D on a Windows 10 machine (x64) and
I can't load a .tif image stack 6.84GB size.
Is there any solution available for windows?
I am trying to load .tif image files because I would like to merge different datasets into separate channels of the same dataset (not blending images, but preserving individual channels for different image stacks of same size). Currently, the only way I have been able to do that is to use the "Import general image series to an image stack" and appending the different .tif files in the "channel" dimension.
I would appreciate any help on that!!
Thank you,
-Mariona
Is there any solution available for windows?
I am trying to load .tif image files because I would like to merge different datasets into separate channels of the same dataset (not blending images, but preserving individual channels for different image stacks of same size). Currently, the only way I have been able to do that is to use the "Import general image series to an image stack" and appending the different .tif files in the "channel" dimension.
I would appreciate any help on that!!
Thank you,
-Mariona