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help > RE: Getting Terafly to work?
Aug 31, 2016 03:08 PM | Alessandro Bria
RE: Getting Terafly to work?
Hi David,
it seems the main problem here is image conversion, which is mandatory for 5D (x,y,z + channel + time) images. Indeed you cannot open unconverted 5D images using the "Open Unconverted Image (3-4D)" menu of TeraFly, which currently works only with single time points (no time series).
As to conversion with TeraConverter, please be sure that you check the "Time series of" checkbox and select the correct format of each file. In your case, this should be "TIFF (3D)" for multipage tiffs, and "Vaa3D raw" for Vaa3d raw files. Then, you should select the folder containing all the time points, each stored in a separate file.
If you don't have the "TIFF (3D)" menu entry, you should convert tiff to raw and then proceed as explained above, or you can use the latest Teraconverter v2.2.2 by building Vaa3D from source code. Please follow the instructions on the Vaa3D wiki at this link.
Also, it could be useful to refer to the Supplementary Text of our Nature Communications's paper (link), which contains the usage manual for TeraFly and TeraConverter (link).
Originally posted by David Dreher:
it seems the main problem here is image conversion, which is mandatory for 5D (x,y,z + channel + time) images. Indeed you cannot open unconverted 5D images using the "Open Unconverted Image (3-4D)" menu of TeraFly, which currently works only with single time points (no time series).
As to conversion with TeraConverter, please be sure that you check the "Time series of" checkbox and select the correct format of each file. In your case, this should be "TIFF (3D)" for multipage tiffs, and "Vaa3D raw" for Vaa3d raw files. Then, you should select the folder containing all the time points, each stored in a separate file.
If you don't have the "TIFF (3D)" menu entry, you should convert tiff to raw and then proceed as explained above, or you can use the latest Teraconverter v2.2.2 by building Vaa3D from source code. Please follow the instructions on the Vaa3D wiki at this link.
Also, it could be useful to refer to the Supplementary Text of our Nature Communications's paper (link), which contains the usage manual for TeraFly and TeraConverter (link).
Originally posted by David Dreher:
Hi everyone,
I'm trying to get Terafly to work as a visualisation tool for my SPIM movies that are way too large to load into memory, but I cannot get it to work.
My 3D stacks are single channel, multi-page TIFFs with 1 file for each time point. I renamed all files like Time_000.tif, Time_001.tif, ... ( Around 6.7GB each, 2048*2048*800)
I tried the following on Mac OS 10.11.6:
Downloaded the binaries, execute the app and later the script inside the .app folder to see error output.
Use Teraconverter to convert the Tiff Stacks to the raw resolution pyramid. I get a seg fault:
./vaa3d_script: line 9: 51907 Segmentation fault: 11 ${MACOS_DIR}/vaa3d $@
Use Fiji to convert Tiff stacks into vaa3d raw files and then use Teraconverter to produce the resolution pyramid results in the same seg fault.
Tried Importing the Tiff folder directly into Terafly via the unconverted data tab.
Produces an error that the folder is missing metadata and then another error that the folder is not starting with RES, when renaming the folder it just produces another error. See attachments.
Tried importing the vaa3d files as unconverted produces a 3D volume that is 2048*2048*11 ( I tried with only 11 time points to save time) And when moving around an error pops up that the raw image has more than a single slice. When I open a single vaa3d files in Fiji they are the correct size. It seems to get confused about the image dimension but there is no Option where I could change thet behaviour.
I then moved to my linux machine and tried again with the binaries. When trying to convert the same data it works for a while and then creates a memory violation access error or seg faults. Though after some files have been processed. Directly importing into Terafly doesn't work and produces errors or also seg faults depending on how I play around.
I then tried to build Vaa3d on the machine from source, the build code runs through but does not create an executable. I attached the output also.
Since I only can attach a single file I made a zip with 3 screenshots and a .txt file with the console output from the build.
Hope you can help me!
Best, David
I'm trying to get Terafly to work as a visualisation tool for my SPIM movies that are way too large to load into memory, but I cannot get it to work.
My 3D stacks are single channel, multi-page TIFFs with 1 file for each time point. I renamed all files like Time_000.tif, Time_001.tif, ... ( Around 6.7GB each, 2048*2048*800)
I tried the following on Mac OS 10.11.6:
Downloaded the binaries, execute the app and later the script inside the .app folder to see error output.
Use Teraconverter to convert the Tiff Stacks to the raw resolution pyramid. I get a seg fault:
./vaa3d_script: line 9: 51907 Segmentation fault: 11 ${MACOS_DIR}/vaa3d $@
Use Fiji to convert Tiff stacks into vaa3d raw files and then use Teraconverter to produce the resolution pyramid results in the same seg fault.
Tried Importing the Tiff folder directly into Terafly via the unconverted data tab.
Produces an error that the folder is missing metadata and then another error that the folder is not starting with RES, when renaming the folder it just produces another error. See attachments.
Tried importing the vaa3d files as unconverted produces a 3D volume that is 2048*2048*11 ( I tried with only 11 time points to save time) And when moving around an error pops up that the raw image has more than a single slice. When I open a single vaa3d files in Fiji they are the correct size. It seems to get confused about the image dimension but there is no Option where I could change thet behaviour.
I then moved to my linux machine and tried again with the binaries. When trying to convert the same data it works for a while and then creates a memory violation access error or seg faults. Though after some files have been processed. Directly importing into Terafly doesn't work and produces errors or also seg faults depending on how I play around.
I then tried to build Vaa3d on the machine from source, the build code runs through but does not create an executable. I attached the output also.
Since I only can attach a single file I made a zip with 3 screenshots and a .txt file with the console output from the build.
Hope you can help me!
Best, David
Threaded View
| Title | Author | Date |
|---|---|---|
| David Dreher | Aug 30, 2016 | |
| Alessandro Bria | Aug 31, 2016 | |
| David Dreher | Aug 31, 2016 | |
| Alessandro Bria | Aug 31, 2016 | |