Mov-IT Interactive Visualization Tool

Installation

1. Download the Mov-IT application

Select the package corresponding to your system and install or uncompress it:

Linux 32

OS X

Windows 32

Note: if there is no cache folder inside the installation directory, pre-run the application (double-click on the executable), leave the Login and Password text fields empty by pressing Ok twice, then quit the application.

2. Download a dataset

Select one or several raw data and digital embryo datasets from the datasets' webpage (Paracentrotus lividus and Phallusia mammillata datasets are smaller, hence faster to download) and unzip their contents in the cache folder, which should now look like this:

3. Run Mov-IT

Double-click the executable and select one of the downloaded datasets from the left-hand side margin. The visualization interface opens, displaying the orthoslices in gray levels and the cell centers as small cubes.

To load your own datasets, click on New experiment instead and select one of two possible source formats:

vtk file (.vtk or .vtk.gz): this option requires to use VTK-formatted datasets that are "homogeneous", i.e. in which the dimensions, format and resolution are constant across all time steps. First, select a VTK or compressed VTK file, then enter a short description for the dataset. Other prompts will request the number of time steps and the interval in milliseconds between two time steps. Finally, your experiment is created and added to the list on the home page.
previously downloaded experiment (local cache): this option is intended for reuse of a local experiment that was already created as above. An initial experiment serving as a model is requested (new label), then another prompt will suggest a new name to label this experiment.

Quick tour

Moving and navigating

To rotate an embryo: click, hold and move the mouse at the same time.
To translate an embryo: hold the ⇑ Shift key and move the mouse (without clicking).
To zoom in/out of an embryo: use the mouse wheel, or hold the Alt key and move the mouse up and down (without clicking).
To navigate along the cell tracking back and forth through time: use the up arrow ↑ and down arrow ↓, or hold the ⇑ Shift key and use the mouse wheel (without moving the mouse).
To focus on one cell: "right-click" on it.
To keep the focus on the same cell along the tracking: hold the ⇑ Shift key while using the up arrow ↑ and down arrow ↓.

Cell tracking

To view the cell tracking: press the slash key /.
To access more tracking view options: point to the Render tab (in the vertical orange-green menu) and check the Tracking box. Use the slider to set the number of time steps to display, and the Forward button to select the navigation mode (forward, backward, or both).

Orthoslices

To view the orthoslices: press the equal key =.
To access more orthoslice view options: point to the Render tab (in the vertical orange-green menu) and check the Orthoslices box. Press % or ch1/ch0 to switch between channels. Check/uncheck the boxes at the end of each axis to activate/deactivate the display of the corresponding plane.
Use the G/V, or T/Y, or R/F keys to move an orthoslice along the x, or y, or z axes respectively.

Tutorial

A menu bar (vertical orange-green tabs) offers access to main properties and functions. Menu tabs are automatically selected by flying the mouse over them.

Info tab

The Info tab displays the number of cells at the current time step, the number of tracked cells with respect to the next time step, and the difference in cell number with the next time step.

Info tab options:

Dividing checkbox: displays the number of dividing cells with blinking highlight in the 3D view.
Dying+lost checkbox: displays the number of lost cells at the next time step with blinking highlight in the 3D view.
Incoming checkbox: displays the number of cells not tracked at the previous time step with blinking highlight in the 3D view.
4D/Lineage button (or L key): switches the display between 4D rendering and lineage tree layout.

Example of lineage tree layout in a digital embryo

Select tab

The Select tab is dedicated to the management of "selections", i.e. groups of cells that can be targeted and labeled with different colors in order to visualize and analyze subpopulations of cells.

To choose a selection in which you want to store a cell population of interest: press the < and > keys. Up to 80 selections can be stored, each under a different color. To change the color of the current selection: click the Change color button.
To add cells to the current selection: press the S key to enter the Select mode, then fly the mouse over each cell center to add it to the current selection. To collect a greater number of cells more quickly: press the Ctrl key and fly the mouse between the centers. Press the S key again to exit the Select mode.
To remove cells from a selection: press the U key to enter the Unselect mode, then use the mouse as above. Press the U key again to exit the Unselect mode.
Selections can be propagated forward to the next time steps with the N key, and backward to previous time steps with the B key.

Select tab options:

As focused button: sets the current selection to the one containing the focused cell ("right-click" on a cell to focus on it).
Erase this button: removes all cells from the current selection.
Erase all button: removes all cells from all selections.
Erase others button: removes all cells from all selections except the current one.
Import from a file and Export to a file buttons: manage external selection file for sharing or backup.

Render tab

The Render tab allows superposing cell centers and trajectories (tracking) with the raw data.

Mov-IT loads .vtk files (raw data) from their directory in the cache. To change the path: click on Manage local data, drag and drop a file from each channel, and click on done.
Raw data can be displayed in orthoslices (2D sections oriented in the xy, xz, and yz planes) or 3D volume rendering. To select a display mode: tick the corresponding box or use the shortcuts (= for orthoslices, @ for volume rendering).

Tracking options:

Press / or check Tracking in the Render tab.
Choose how many time steps to visualize and the mode (forward, backward or both) by clicking on Forward.
Show Selected cells only: displays only the cells that are part of a selection (see Select tab).

Orthoslices options:

Use the G/V, or T/Y, or R/F keys to move an orthoslice along the x, or y, or z axes respectively, or move the corresponding slider. You can hide an orthoslice by ticking the checkbox.
The contrast can be adjusted using the corresponding slider. You can toggle between channels using the ch1/ch0 button or the % key.
When cells are densely packed you can limit the visualization and reduce the number of displayed cells by clicking on Ortho neighborhood only. Only the cells that are close to the (xy) orthoslice will be displayed.

Volume rendering options:

Up to 20 different color maps (lookup tables) can be chosen with the slider.
The alpha channel can be modified through the bottom histogram.

Extra tab

Extra tab options:

Reset camera button: centers the camera on the origin.
Auto Swing checkbox: gives the camera a slow circular motion around its current position.
Axes, Center and Bounds checkboxes: displays numerical and graphic information about the coordinates and the coordinate system.
Background color button: changes the color of the background (default is black).
Save a picture button: takes a screenshot of the application and stores the file in the application folder.
Shortcuts button: displays a help list of command shortcuts on the right-hand side margin of the screen.
Limit time to t<n> button: ignores time steps after the <n>th one.

Graph tab

Charts options:

Basics: plots the number of cells over time.
Selected cells: plots the number of selected cells over time.
Annotated cells: plots the number of annotated cells over time.
Cell life: plots the inter-division lifetime of each cell over time.
Daughter lifetime ratio: same as Cell life except values are divided by the total number of time steps.
Speed: plots the velocity of each cell over time.

Colormap options (to color cells by their features):

Selected cells only: coloring will affect selected cells only.
Speed: colors cells according to their velocity and plots the velocity average in the bottom-right corner of the screen.
Life length: colors cells according to their inter-division lifetime.
Cell life
Selection dispersion: colors cells according to their dispersion.
Distance to closest: colors cells according to their distance to the nearest neighbor.
Selection color
Generation: colors cells according to their number of divisions along the lineage branches.
Direction: colors cells according to their direction of movement.

Movie tab

You can create an image sequence using Mov-IT very easily. Choose a time step of interest, camera position and orthoslices then press the I key to add the first frame of your movie. You can add as many frames as you want with different camera positions, orthoslices or time steps. Once at least two frames have been added, the extended menu appears. Press D to remove a frame, or O to update it. You can switch between frames using ← or →.

Mov-IT will automatically add frames between keyframes you added. The default number of frames added for interpolation is 40, but you can increase or decrease this value as you wish (+ and - keys).

Press M to create the image sequence. Files will be stored in the Mov-IT folder. You can use image Software such as Fiji or ImageJ to create a movie.

Check tab

Warning: there is no undo command.

Annotation mode (click on the check box Enable Annotation) allows you to access the tracking information, to correct manually an erronated link or to create an new link (a link represents the correspondence between two cells of consecutive time steps).

You can confirm or infirm centers detected automatically (if a center is correct hit A, if it is incorrect hit Z). You can add centers with W or move a focused center (right click a cell) with J. You can also cut, modify or add links between related centers along the timeline.

When the enable annotation mode is active, the focus stays on the chosen cell when you move through the timeline. When you click on a center, a transparent cube appears. When you move forward or backward along the timeline (↑ and ↓ arrows) the cube follows the tracking links. This allows you to follow a chosen cell along the timeline. To be sure that you are really following the cell, you can superimpose raw data and centers (see Render tab).

Addition of new centers/manual tracking

If some centers are missing or if you want to perform a manual tracking, move the cursor over a cell (visualized with orthoslices) and hit W. If the center is correct and you wish to annotate it, hit A. As for the automatically detected centers, you can displace them hitting J.

Correction of links

Focus on a center by right-clicking on it. When you move from the current step to the next one (↑ and ↓key) and the link seems correct (according to the raw data), you can positively annotate it with the Q key. If the link is incorrect click on delete mother and child (delete the link between t and t+2) or click on delete tracking to delete the link between t and t+1 only.

To add a new link, point on a center at each time step and hit S. To finalize the addition of the links, hit X.

When a cell divides, select the mother and the two daughters (not more) and hit X.

Annotate mitosis

It allows you to display a selection of all the detected mitoses. Then compare with the raw data and validate the mitoses by hitting I or clicking on validate mitosis. You can switch between dividing cells using ← and → arrows.