Dear sir,

I was trying to open the testing data from your github website (https://github.com/Vaa3D/Vaa3D_Data/rele...) with the Ultratracer in Linux but failed, possibly because the data size was too big (2.1G, while the max size suggested by the Linux error message is 1.5G, if run on a 32bit machine). May I ask is there a way to fix this problem? Thanks a lot for your help.

1. Use "TeraConverter" (under Advanced --> Big-Image-Data) to convert your file to TeraFly format.
2. Open your converted TeraFly format image using "TeraFly" (under Advanced --> Big-Image-Data).
3. In TeraFly mode, use the menu in the left bar to define a soma marker location and save the annotation including three files (xx.ano, aa,ano.apo, and xx.ano.swc).
4. Open "ultratracer" plugin, keep "va3draw/raw image or tc file" empty. select the saved "xx.ano.apo" as the "marker file", the highest resolution folder as the "terafly format file".
5. Run the plugin.

All TeraConverter and TeraFly related questions, please check our paper (http://www.nature.com/nmeth/journal/v13/...)

Thanks,

Zhi

Thank you very much for your detailed instruction. I will try it later.

Dear sir,

How to use 'ultratracer' for the 'TeraFly' opened file?

I don't really understand this sentence in your last reply: '4. Open "ultratracer" plugin, keep "va3draw/raw image or tc file" empty. select the saved "xx.ano.apo" as the "marker file", the highest resolution folder as the "terafly format file".'

I have converted my file to TeraFly format, then opened it in TeraFly, and in TeraFly mode, a soma marker have be defined and saved, there are xx.ano; xx.ano.apo; and xx.ano.swc 3 files in the destination folder. so far, there is no fault.

Then I open 'ultratracer' plugin (vaa3d-->plug_in-->neuron_tracing-->ultratracer-->tracer_MOST), the dialog box popped said: 'No markers in the current image, please select a marker'.

There must be something I missed, like 'Open "ultratracer" plugin, keep "va3draw/raw image or tc file" empty. select the saved "xx.ano.apo" as the "marker file" '. but I don't know how to do that.

Thanks,

Zhangzhou

Thanks for choosing UltraTracer. Please close all opened image, and try the plugin again. Then you will see the the Input Parameters Dialog Box.

It works, thanks!

Dear sir,

Does Vaa3D (or TeraFly) support 16-bit-images visualization?
If it does, how to adjust the Minimun and Maximun gray value to display?

My raw image is 16-bit,but the gray value of the signals is not very high, in consideration of high dynamic range of the 16-bit image, I have to change the the Minimun and Maximun gray value for better display, but I couldn't find such a tool in Vaa3D like in ImageJ adjust brightness and contrast tool.

Thank you again for your kind help!

Best,

ZhangZhou

You can try to rescale the image first. Attachment is one option.

Originally posted by Zhang Zhou: