brain-stitcher 1.3.2

Stitcher package is a 3D mesh builder

It was developed by metaBIO lab member Heitor Gessner as part of his master thesis. The main usage is for recreating brain models from rare species, i.e., especies with low number of spiciements.

It provides 3 classes:

• Points()

• Perimeters()

• Surface()

Each Periemeter is a collection of Points. Each Surface is a collection of Perimeters. For the points in points, it is expected to have a 3D coordinate reference for each point that delimits a plane contour. The contours are made by manual or automatic segmentation, in the case of brains. This can be done in softwares such as ImageJ, Horos or Osirix - and than exported as a json file.

Version 1.1:

-New super resolution method using Fourier Transform -Fixed fix_intersection() method from Perimeter() to properly handle rare parallel lines case

Version 1.2:

-FIX: Point division by number added as operation (division) -NEW: Perimeter legth added -NEW: estimation of volume and lateral area by numerical approximation prior to the reconstruction (doi: 10.3389/fnana.2013.00028) -NEW: report of possible topological artifacts after build the 3D mesh

Version 1.2.1:

-CHANGE: fixing the intersection is optinal when making a new Perimeter

Version 1.2.2:

-Fix: loading from cache now works as expected -NEW: Perimeter.remove_by_angle(limit_in_radians) method to remove vertices that with angle<limit

Version 1.2.2.1:

-Fix: Intersection check limit (reconstruction.Surface.intersection_limit) is now a property of Surface intead of being hard coded

Version 1.2.3:

-NEW: Added Surface.self_intersection boolean property to report problematic surface build

Version 1.3:

-Fix: remove_overlap was improved and now can handle multiple overlaps on the same spot

Version 1.3.1:

-Fix: islands_ensemble now doesn’t create self intersection anymore

Version 1.3.2:

-Fix: fix_intersection in Perimiter class didn’t update de area vector, now it does