tferr/hipnat

:microscope::deciduous_tree::computer: hIPNAT: Image Processing for NeuroAnatomy and Tree-like structures (Archived)

hipnat's Issues

Strahler: Ensure Users are aware of single-arbor restrictions

From @tferr on March 7, 2016 4:38

It should be more obvious for users that results assume images with a single tree. Discussed here.

Copied from original issue: tferr/Scripts#15

Skeleton rendering of 3D traces files fails

Things seem to work ok if 2D traces, but not with 3D traces...

Routine for removal of the patch pipette

We should include a routine for removal of pipette artifacts for neurons intracellularly filled during patch recordings. In the past this may have been implemented, including

1. Neura (Relevant source)
2. Orion, closed source(?)

Strahler: Improve 3D analysis

Right now when analyzing 3D arbors, we infer orders from Z-projections. While in practice this probably works fine, there is really no reason to do so. See also #2.

Strahler: Extend root detection to 3D

From @tferr on January 2, 2015 19:34

This is just an immediate followup to #4. Now that root-detection is working, it should be extended to 3D.
In order to implement it, we will need to:

• Check if ROI is associated with all slices or just one (discussed here)
• Ignore end-points above/below the ROI, as needed
• Extend ImageProcessor operations to stack, as needed

Copied from original issue: tferr/Scripts#8

Render multiple SWC files: Wrong offsets

Reported by Volko Straub:

converting the Traces file to a SWC file, results in a breakup of the original trace and when it is re-assembled with the 'Render multiple SWC files', the individual components are placed in different positions. This is illustrated in the attached screen shot at the bottom, which shows the original SNT traces on the left and the output from 'Render multiple SWC files' of the same Traces file after converting to SWC files on the right.

Traces.zip