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Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.

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![Mastodon logo](https://raw.githubusercontent.com/mastodon-sc/mastodon/master/doc/Mastodon-logo-512x512.png)

Read the user and developer documentation [here](https://mastodon.readthedocs.io/).

# Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.

Modern microscopy technologies such as light sheet microscopy allows live sample *in toto* 3D imaging with high spatial and temporal resolution. Such images will be 3D over time, possibly multi-channels and multi-view. Computational analysis of these images promises new insights in cellular, developmental and stem cells biology. However, a single image can amount to several terabytes, and in turn, the automated or semi-automated analysis of these large images can generate a vast amount of annotations. The challenges of big data are then met twice: first by dealing with a very large image, and second with generating large annotations from this image. They will make interacting and analyzing the data especially difficult.

**Mastodon** is our effort to provide a tool that can harness these challenges.

## *Warning.*

Despite the naming of the artifacts and the apparent usability of the software, *Mastodon is still in alpha stage, not released, not published and not supported* at the present time.

## Mastodon goals.

The goals of Mastodon are the following:

- **Interactive** browsing, inspection and navigation through the image data. Fast and responsive.
- Build **tracking and lineage data** from images.
- **User-friendly** framework to navigate through this data. Easy to relate spatial information with hierarchical information. Easily orient the user in a possibly very large annotation.
- "Point-wise" **interactive editing** of the tracking and lineage data. Manual curation.
- **Semi-automatic and fully automatic tracking**.
- **Numerical features** and statistics on tracking data. **Tagging of this data**. Tags and numerical features can then be used to to enrich the visualization.
- **Extensible**: a 3rd party can build plugins for Mastodon:
  - Custom numerical feature analysers;
  - Custom tracking algorithms (detection and particle-linking algorithms);
  - General-use plugins.

## Mastodon components.

![BDV and TrackScheme](https://raw.githubusercontent.com/mastodon-sc/mastodon/master/doc/Mastodon_BDV_and_TrackScheme.png)

### BDV windows.

Display image data and overlay the tracking data. Single objects (spots or links) can be individually edited.

![Multi-view image in BDV](https://raw.githubusercontent.com/mastodon-sc/mastodon/master/doc/Mastodon_BDV-moving.png)

![Single track in BDV](https://raw.githubusercontent.com/mastodon-sc/mastodon/master/doc/Mastodon_BDV-editing.png)

### TrackScheme windows.

TrackScheme is used to display a hierarchical view of the lineage data. The tracks are arranged from left to right, and time is laid out from top to bottom.

![TrackScheme example 2](https://raw.githubusercontent.com/mastodon-sc/mastodon/master/doc/Mastodon_TracSchemeColoring_02.png)

![TrackScheme example 3](https://raw.githubusercontent.com/mastodon-sc/mastodon/master/doc/Mastodon_TracSchemeColoring_03.png)

## Mastodon technologies.

Mastodon is a Java software that relies on several technologies to achieve these goals, specially developed for it.

*Interactive visualization and navigation of large images thanks to the BigDataViewer* ([BDV](https://imagej.net/BigDataViewer). Any file that can be opened in the BDV will work in Mastodon (BDV HDF5 file format, KLB, Keller-Lab Blocks file format, N5 file format, ...). These file formats enable interactive visualization of multi-view TB dataset at the one-time cost of a file conversion. Also, they can be exploited for efficient image processing in special cases, taking advantage of multi-scale pyramidal representation and blocks decomposition.

*[Mastodon-collection](https://github.com/mastodon-sc/mastodon-collection): a high performance framework to manipulate collections of data*. Mastodon-collection was developed specifically for this project. It offers an in-memory compact layout storage of objects. Mastodon collections have a much smaller memory footprint. Objects in a mastodon collection are contiguous in memory. Thanks to CPU cache and [data locality](http://gameprogrammingpatterns.com/data-locality.html), iterating these collections is much faster than classical object collections. Mastodon-collection also offers techniques to do garbage-collection-free manipulations in Java, considerably improving the responsiveness of applications based on it.

*[Mastodon-graph](https://github.com/mastodon-sc/mastodon-graph): a data structure based on mastodon-collection, and optimized for lineage and tracking data.* Mastodon-graph is a graph library based on mastodon-collections, that underlies the data model of Mastodon.

*Efficient retrieval of objects in space and time*. User interactions with tracking objects rely on [Kd-tree search on convex polytopes](http://fly.mpi-cbg.de/~pietzsch/polytope.pdf).

*Level of detail to display large number of objects*. TrackScheme automatically adapts the level of detail while displaying data at varying scales.

## Usage.

### Actions and keyboard shortcuts.

The keyboard shortcuts listed below are valid for the _default_ key-map.

#### BigDataViewer (BDV) windows.

##### Moving around and display in BDV windows.

| Action | Key |
| -------------------------------- | ------------------------------------------------------------ |
| _View._ | |
| Move in X & Y. | Right-click and drag. |
| Move in Z. | Mouse-wheel. Press and hold shift to move faster, control to move slower. |
| Rotate. | Click and drag. The view will rotate around the location you clicked. |
| Align view with X / Y / Z axes. | - Align with XY plane: `Shift-Z` - Align with YZ plane: `Shift-X` - Align with XZ plane: `Shift-C` or `Shift-Y` The view will rotate around the location you clicked. |
| Zoom / Unzoom. | `Control-shift mouse-wheel` or `Command-mouse-wheel`. The view will zoom and unzoom around the mouse location. |
| _Time-points._ | |
| Next time-point. | `]` or `M` |
| Previous time-point. | `[` or `N` |
| _Bookmarks._ | |
| Store a bookmark. | `Shift-B` then press any key to store a bookmark with this key as name. A bookmark stores the position, zoom and orientation in the view but not the time-point. Bookmarks are saved in display settings file. |
| Recall a bookmark. | Press `B` then the key of the bookmark. |
| Recall a bookmark orientation. | Press `O` then the key of the bookmark. Only the orientation of the bookmark will be restored. |
| _Image display._ | |
| Select source 1, 2, ... | Press `1`, `2`, ... |
| Brightness and color dialog. | Press `S`. In this dialog you can adjust the min & max for each source, select to what sources these min & max apply and pick a color for each source. |
| Toggle fused mode. | Press `F`. In fused mode, several sources are overlaid. Press `Shift-1`, `Shift-2`, … to add / remove the source to the view. In single-source mode, only one source is shown. |
| Visibility and grouping dialog. | Press `F6`. In this dialog you can define what sources are visible in fused mode, and define groups of sources for use in the grouping mode. |
| Save / load display settings. | `F11` / `F12`. This will create a XYZ_settings.xml file in which the display settings will be saved. |

##### Manual editing and navigation in BDV windows.

| Action | Key |
| ----------------------------------------- | ------------------------------------------------------------ |
| _Editing spots._ | |
| Add a new spot. | Press `A` with the mouse over the desired location. |
| Remove a spot. | Press `D` with the mouse inside the spot to remove. |
| Increase / Decrease the radius of a spot. | Press `E` / `Q` with the mouse inside the spot. `Shift-E` / `Q` increase / decrease the spot radius by larger steps. `Control-E` / `Q` enlarges the spot radius by finer steps. |
| Move a spot. | Press and hold `space` with mouse inside the spot to move, and move it around. |
| _Creating links between spots._ | |
| Create a link between two spots. | Press and hold `L` with the mouse inside the source spot. The BDV moves to the next frame. Release `L` when inside the target spot. Press and hold `Shift-L` to do the same, but linking to the previous frame. |
| Remove a link. | Press `D` with the mouse on the link to remove. |
| Create a spot linked to a spot. | Press and hold `A` with the mouse inside the source spot. The BDV moves to the next frame. Release `A` at the desired position. A new spot is created, linked to the source spot. Press and hold `Shift-A` to do the same, but linking to the previous frame. |
| _Selection editing._ | |
| Add a spot / link to the selection. | `Shift-click` on a spot or a link to add / remove it to / from the selection. |
| Clearing the selection. | Click on an empty place of the image. |
| Remove selection content. | `Shift-delete`. |
| _Undo / redo_. | |
| Undo. | `Control-Z`. |
| Redo. | `Control-shift-Z.` |

#### TrackScheme windows.

##### Navigation through lineages in BDV and TrackScheme windows.

| Action | Key |
| ------------------------------------------ | ------------------------------------------------------------ |
| _Navigation._ | |
| Navigate to parent / child in time. | `↑` / `↓`. Select and move to the spot linked to this one in the previous / next time-point. Press `shift` to also add it to the current selection. |
| Navigate to sibling. | `←` / `→`. Select and move to the sibling of this spot. A sibling is another spot from the same lineage in the same time-point. Press `Shift` to also add it to the current selection. |
| Navigate to branch parent / child in time. | `Alt + ↑` / `↓`. Select and move to the parent / child branch. A branch starts and ends with a division or fork in the lineage. Press `Shift` to also add it to the current selection. |
| Navigate to spot / link. | `Double-click` on the spot / link. |
| _Selection._ | |
| Select all parents. | `Shift + ⇞`. Select all the parents of this spots, that is all the spots in its lineage backward in time. |
| Select all children. | `Shift + ⇟`. Select all the children of this spots, that is all the spots in its lineage forward in time. |
| Select all lineage. | `Shift + space`. Select all the spots of this spot lineage. |

##### Moving around in TrackScheme windows.

| Action                  | Key                                                          |
| ----------------------- | ------------------------------------------------------------ |
| _View._                 |                                                              |
| Move around.            | `Right-click` and `drag` or `mouse-wheel`.                   |
| Zoom / unzoom in X.     | `Shift mouse-wheel`.                                         |
| Zoom / unzoom in Y.     | `Control-mouse-wheel`.                                       |
| Zoom / unzoom in X & Y. | `Control-shift-mouse-wheel`.                                 |
| Full zoom, full unzoom. | Press `Z`. The view zoom at max level to the mouse location. Pressing `Z` again to unzoom fully. |
| Zoom in a box.          | Press and hold `Z`, then drag a box. The view will zoom to the box. |

_TrackScheme box zoom:_
Drag a rectangle with the `Z` key pressed. TrackScheme will zoom to this rectangle. A press of `Z` fully zoom to designated location.
If TrackScheme is fully zoomed, a tap of `Z` unzoom fully.
![TrackScheme_ZoomBox](https://user-images.githubusercontent.com/3583203/32853983-6bfdd534-ca3d-11e7-8437-ec76eb04ae61.gif)

##### Manual track editing in TrackScheme windows.

| Action | Key |
| ----------------------------------- | ------------------------------------------------------------ |
| _Editing spots._ | |
| Remove a spot. | Press `D` with the mouse inside the spot to remove. |
| Edit the label of a spot. | Press `Enter` when a spot is focused, then enter its label and press `Enter` to validate. |
| _Creating links between spots._ | |
| Create a link between two spots. | Press and hold `L` with the mouse inside the source spot. Release `L` when inside the target spot. |
| Remove a link. | Press `D` with the mouse on the link to remove. |
| _Selection editing._ | |
| Add a spot / link to the selection. | `Shift-click` on a spot or a link to add / remove it to / from the selection. |
| Select all in a box. | `Click and drag` a box. `Shift-click and drag` to add the content of the box to the current selection. |
| Clearing the selection. | `Click` on an empty place of the image. |
| Remove selection content. | `Shift-delete.` |
| _Undo / redo._ | |
| Undo. | `Control-Z`. |
| Redo. | `Control-shift-Z`. |

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