Hi all,

I'm new to tracing neurites and I have a bunch of data with spinal cord explants on muscle cells.  The images are 2D tiled images that have a lot of uneven background and some really faint neurites.  No matter how I process them, I'm not able to get all the neurites in the image.  Do you have suggestions for how I can use 3D programs like APP2 and UltraTracer for 2D?  Do the algorithms automatically look for z-stacks?  Can that be overcome?

Thank you for your help,

Juanita

Can you provide one example image for us to check first? Thanks.

Zhi

By the way, UltraTracer with base tracer APP2 can trace large-scale 2D images directly. However, if the background is uneven, the image may need per-processing.

Use the adaptive automatic thersholding (a plugin in vaa3d) to try first ....


Originally posted by Zhi Zhou:

Here is an example image.

I have checked the image. Here are my suggestions:
1. You don't have to use Ultratracer. APP2 should be able to handle this image directly.
2. Before running APP2, try to use our "anisotropic filer" plugin to pre-process the image first. The plugin is under "Plug-in" --> "Image_filer" --> "anisotropic_filter" --> "anisodiff_general".
3. Try different thresholds in APP2 to obtain better results.
4. If signals are fragmented, it may hard to trace automatically. Instead, you can use Vaa3D Virtual finger function to semi-automatically trace these structures.  Here is one related paper for your reference (https://www.nature.com/articles/ncomms53...).

Hope it helps.

Zhi