search

Neural-Systems-at-UIO / MeshView-for-Brain-Atlases

WebGL based mesh viewer with solid slicing and point cloud support. User documentation https://meshview-for-brain-atlases.readthedocs.io
MIT License
7 stars 2 forks source link

MeshView - enhancements #6

Open marovst opened 3 years ago

marovst commented 3 years ago

1). Feedback based on recent testing of the updated version of MeshView: a) The point coordinates change position in the viewer when the surrounding structure is turned off. b) It would be preferable with advanced camera control. E.g rotation in a single axis/plane or specified point coordinate. c) To specific cut surface meshes in user-specified planes.

2). We need a mesh file for the pontine nuclei surface on the right side in some standard file format, with mesh coordinates compatible with the point coordinates that we have extracted from the atlas using LocaliZoom. This to allow us to visualize the surface and the points in another software (Imaris or similar).

3). We need more custom versions of the local MeshView with a surface of the CPu, thalamus, and superior colliculus. Surface on the right and the left side, as for the pontine nuclei.

Tevemadar commented 3 years ago

1a) could you point me to an actual pointcloud you are working with? 1b) may be possible 1c) I don't understand this one, the cut surface already contains only the meshes which are toggled "on" (opaque) 2) NESYS_Tools\Gergely\Meshes\ABAv3-2017-Hemispheres contains mesh sets for the hemispheres in STL format 3) 6 new mesh-sets have been added: https://www.nesys.uio.no/MeshView/meshviewy.html?atlas=ABA_mouse_v3_2017_CPuL CPuR, SCL, SCR, ThalL, and ThalR.

marovst commented 3 years ago

1) a) 141602484_M2_spread.txt My take is that when all the structures is off, the viewer used the limits of the whole brain atlas as reference. Thus, the point clouds shifts when I switch on or off my reference structures as they are smaller than the whole brain (e.g. pontine nuclei). It also seems that the reference structure is the center of the view. Would this be correct? c) We would like to cut the regional mesh like we cut the point clouds. E.g. when we cut the point clouds we also cut through the mesh in such way that we show an outline of the mesh like the slice seen for the point cloud. This is something we can work around for now.

2) and 3) thank you. The new meshes looks great and is exactly what we were looking for.

Image for 1a): Outline_moves

Majpuc commented 3 years ago

Status on 03.09.2021. Due to deadlines on M18, we need to prioritize other developments. This will be addressed later.

Majpuc commented 1 year ago

This issue is not present in the released versions of MeshView. Is this correct? @Tevemadar