help
help > RE: loading 4D data
Jul 19, 2016 09:07 AM | Hanchuan Peng
RE: loading 4D data
So far the only "format" we load 4D data will be (1) organizing
each time point as a separate image stack, which can have xyz
information and even color information (thus itself is a 4D stack).
The file format can be anything Vaa3D supports, e.g. tiff, vaa3d's
own raw format, .... (2) each such time point file should be named
as sth like xyz_00001.tif, xyz_00002.tif, .... .
If the overall dataset is small enough to be loaded completely into computer memory, you can load such data using Vaa3D main data importing tool (from main menu).
If the overall dataset is large enough so that it is impossible to load into the memory, you need to convert the dataset into terafly format. Go to main menu and choose Advanced -> Big Image Data -> TeraConverter and then after the data conversion, use TeraFly tool to load the data.
Best,
-Hanchuan
Originally posted by raju bhai:
If the overall dataset is small enough to be loaded completely into computer memory, you can load such data using Vaa3D main data importing tool (from main menu).
If the overall dataset is large enough so that it is impossible to load into the memory, you need to convert the dataset into terafly format. Go to main menu and choose Advanced -> Big Image Data -> TeraConverter and then after the data conversion, use TeraFly tool to load the data.
Best,
-Hanchuan
Originally posted by raju bhai:
Hello,
I am having 4 dimensional image in the format of .dat file Extension(Binary Data). Could you please tell me the solution to how to load the Image(.dat file) to VAA3D.
Thanks in advance.
Originally posted by Hanchuan Peng:
I am having 4 dimensional image in the format of .dat file Extension(Binary Data). Could you please tell me the solution to how to load the Image(.dat file) to VAA3D.
Thanks in advance.
Originally posted by Hanchuan Peng:
Ok, normally we
store a 3D image stack, which includes X,Y,Z, into one SINGLE file.
This can be stored as 3D TIFF format, or as a Vaa3D's Raw file.
Each file can also has a color channel (which will make it actually
a 4D image stack).
Then, each time point corresponds to a single image stack file. Each image stack has the naming convention xxx_001.tif, xxx_002.tif, ...
Then use the import function in my last msg to load the data into "Color Channel". Suppose you have 100 time points, each is a 4D image stack of the size 512 x 300 x 400 x 2 (in the order of X, Y, Z, and C). Then after importing, in the tri-view main window you will see the loaded data has 2*100 = 200 color channels. Ignore that, as the software actually knows the loaded data has 100 time points! Then when you open the 3D viewer window, you can see the 3D rendered data has 100 time points and 2 color channels, and 400 z-slices!
-Hanchuan
Originally posted by Crystal Davey:
Then, each time point corresponds to a single image stack file. Each image stack has the naming convention xxx_001.tif, xxx_002.tif, ...
Then use the import function in my last msg to load the data into "Color Channel". Suppose you have 100 time points, each is a 4D image stack of the size 512 x 300 x 400 x 2 (in the order of X, Y, Z, and C). Then after importing, in the tri-view main window you will see the loaded data has 2*100 = 200 color channels. Ignore that, as the software actually knows the loaded data has 100 time points! Then when you open the 3D viewer window, you can see the 3D rendered data has 100 time points and 2 color channels, and 400 z-slices!
-Hanchuan
Originally posted by Crystal Davey:
1. I mean X,Y,Z, and T, where T is time.
2. What I am unsure of is how to sequence the files since I have Z and T. For each Z there are multiple Ts so how do you sequence the files? So in the example of xx_01.tif, xx_02.tif are these different time points or different Z slices?
Thanks,
Crystal
2. What I am unsure of is how to sequence the files since I have Z and T. For each Z there are multiple Ts so how do you sequence the files? So in the example of xx_01.tif, xx_02.tif are these different time points or different Z slices?
Thanks,
Crystal
Threaded View
| Title | Author | Date |
|---|---|---|
| Crystal Davey | Jan 28, 2013 | |
| Hanchuan Peng | Jan 28, 2013 | |
| Crystal Davey | Jan 28, 2013 | |
| Hanchuan Peng | Jan 28, 2013 | |
| raju bhai | Jul 19, 2016 | |
| Hanchuan Peng | Jul 19, 2016 | |
| raju bhai | Jul 25, 2016 | |
| Alessandro Bria | Jul 25, 2016 | |
| Hanchuan Peng | Jul 25, 2016 | |