Introduction and Help

Quick Start

Start with a 3D image stack, it can have multiple time frames, but should be single channel. The image properties need to contain correct pixel dimensions. Then the plugin can be ran.

Once the plugin start there will be two windows: a 3D screen, which should be empty, and a control panel with buttons (described below). Click on the button show volume, and a representation of the image stack should appear in the 3D window. Use the -/+ values to adjust the maximum and minimum cutoffs to improve the display.

The next step would be to create a mesh, this can be accomplished by clicking 'initialize mesh...' A dialog will appear with three orthogonal views of the image. Clicking on one of the views will start creating a sphere, clicking again will finish the sphere. The goal is to contain the desired shape in spheres. The spheres position and radius can be adjusted with the blue handles.

Once the shape is close enough, clicking finish will create a mesh. To have the mesh deform to the image, the parameter "image energy" needs to be adjusted, usually start with a small value around 0.001 and click "deform mesh". The mesh will be attracted to local bright features. If the mesh deforms too much, then click stop, got to the edit menu and select undo. Increase the gamma factor (multiply by 10) and try again. The mesh should deform slower, and hopefully improve.

Button Descriptions

previous frame.

next frame

Show volume

Shows volume in 3D window

vol-contrast

Adjust contrast

Initialize Mesh...

open intialize mesh tab.

Deform

Deform selected mesh until stop is pressed.

clear mesh

removes the select mesh

connection remesh

Remesh connections by splitting long connections and removing short connections. Uses the values min length and max length.

raycast remesh

remeshes using a raycast technique.

show forces

shows the external forces on mesh

x

removes force arrows.

show plane

Shows a plane where the furrow plane is positioned.

split mesh

splits the currently selected mesh into two meshes. neither mesh will be associated to a track.

center

centers the furrow to either the center of the selected mesh, or the center of the image.

init

opens a dialog for initializing the furrow location and direction.

select

starts a modification session. nodes can be selected for sculpting *advanced*

sculpt

for moving individual nodes by moving a cursor.

cancel

cancel mesh modification

finish

commit changes made by scuplting.

Parameters Descriptions

gamma

Slows deformations, makes algorithm more stable. Default 1000

alpha

Stretching stiffness. Default 1.0

pressure

Pushes mesh out, (or in if negative.) Small values will cause mesh to shrink slower, large values will cause meshes to grow. Default 0.

steric neighbors

will cause meshes to repel each other. With a value of zero neighbors are completely ignored. Any non-zero value causes all mesh interactions to be checked. This can be slow. Default 0.

divisions

A new mesh starts with 20*4^N triangles. Default 2.

beta

A curvature smoothing term. A small value is "nice" but not too necessary. A large value can be non-intuitive. Default 0.1

Menu Item Descriptions

file

Open image

Opens an image for segmenting

Select open image

Switches to an openned image.

import virtual

Opens an image virtually for segmenting. (Works with .h5 files)

save meshes as

Saves the current meshes.

save

Saves meshes to a previously used file

load meshes

Load meshes

Save parameters

Saves the deformation parameters.

Load parameters

Loads parameters from a saved file.

Start new meshes

Clears the current meshes. Starts over.

edit

undo

undo a previous action

redo

redo an undone action

mesh

export as stl

save meshes to an stl file.

export as wireframe stl

a transformed mesh.

export as ply

saves meshes to a ply file.

trackmate->export as TmXml

creates a trackmate compatible file with x,y,radius values derived from meshes.

trackmate->import From TmXml

loads spherical meshes from trackmate file.

trackmate->track from TmXml

updates the current tracking information to be consistent with TmXml file.

load furrows

loads furrow plane positions from a file.

save furrows

saves furrow plane positions to a file.

track forwards

copies the current mesh to the next frame and links it in the same track.

track backwards

copies the current mash to the previous frame and links it to the same track.

tools

Create binary

creates a binary image of the current selected mesh

create mosaic

creates a labelled image of all existing meshes.

measure all volumes

measures all of the mesh volumes.

measure selected

meshes properties of the currently selected mesh.

measure obscured

looks at mesh surface and touching surfaces.

furrow values

the normals and positions of the furrow.

import meshes

loads meshes from a file.

import from open image

loads meshes from a file, attempts to align geometry.

manage tracks

starts the track-manager tab

Record snapshots

records snapshots of the movie

javascript console

starts the javascript console.

remote prediction

experiments: sends the image to a tensorflow server for processing.

substitute data

substitutes the current image data with other data. Can be used for processing a single frame.

Introduction