"The king is dead, long live the king!"

10-11-2024: This project is considered deprecated in favor of collaborative tracking based on GIT. It has also disappeared from Fiji update sites. If you still want to use it, you must compile it from the sources here, or ask ulman při fi.muni.cz.

What is mastodon-collaborative?

A suite of Mastodon plugins originally developed to foster collaborative tracking.

The idea

The original purpose of this project was to enable tracking cells in the same image data by multiple users (collaborators) independently, that is, on their own laptops at their own pace. To make this effort an efficient one, ideally users work in "separate corners" of the data so that no cell is tracked twice. Users then somewhat regularly submit their current state of the work to a server.

The server is only a repository of tracking data from multiple users. It collects contributions from users and offers it to anyone to download and to incorporate into one's own tracking. Mastodon features simple-to-use plugins for exactly these tasks. By design, the server does not automagically merge anything into one giant tracking as this process can become fragile and must be supervised if you want to trust the outcome of the collaborative tracking.

This concept requires a bit of an organization. Ideally there is a project leader that

• prepares the Mastodon project,
• defines "separate (non-overlapping) corners" in the data,
• distribute project data to collaborators,
• explains and assigns work to collaborators,
• somewhat regularly merges recent contributions from the collaborators
  to check for issues and to detect overlaps rather soon,
• stops the collaboration and merges to obtain the final tracking.

To avoid having (potentially large) image data copied on every laptop, one may want to set up a BigDataServer to host the image data, and adjust Mastodon project path accordingly. Collaborators, when tracking, download online a piece of the data that is currently processed (displayed) in their laptops.

Here it is explained in 2.5 min long video-presentation.

The snapshots

At the heart of these plugins is the ability to create-and-store a snapshot of an annotation of one's own images, as well as to load-and-merge-in a snapshot. The annotation consists of a lineage trees and tag sets, it does not involve the image data per se. The snapshot of an annotation is the exact content of it (all spots and their positions, labels, colors and links) available for the given images at the given time.

A snapshot can be understood as a lightweight alternative to saving the full project. The snapshot itself does not hold any reference to the original project -- one can, for example, merge snapshot from different project into a current one.

Snapshots can be used to store progress of an on-going annotation, can be used as named points of restore, and can be exchanged among annotators -- collaborating Mastodon users.

The snapshot files use .mstdn extension whereas the full Mastodon project files are using the .mastodon extension.

The server

The server is merely a convenient point of exchange of snapshots (or any files), all organized into multiple projects.

To have own server running, one needs to have the following:

• Hosting computer accessible on a network
• Java 1.8 or newer installed
• Fiji with Mastodon installed
• Folder where server data will be stored

The hosting computer can be anything where Java runs. In particular it can be Windows, Mac or Linux computer. And it can run only on local network unless one wants to enable his collaborators to contribute from their homes or invite collaborators from different institutions. In the latter two cases, please refer to your system administrators to help you start the server on appropriately accessible computers (e.g., via VPN, or with public IP address).

To start the server, one only needs to know how to open a command line, which could be named variously in your operating system such as console, terminal or shell. And then look here to find the one-line command to start the server.

It could be worthwhile to serve your image data too.

The project

Clearly, one server has to serve multiple collaborative endeavours, which is to say, to serve multiple projects. It must separate and protect them from each other. Here, it is achieved very straightforwardly.

A project is defined with a string, sequence of characters without blank spaces. Examples can be from simple nickname-likes, e.g., "thirdEmbryo", to rather descriptive ones such as "VladoLab_exp33_DAPIstainedNuclei_t2min_temp36C".

The string addresses a project. Whenever collaborators interfere with the server, this string needs to be passed along for the server to understand which project is the current communication related to. Technical details regarding projects are summarized on another page.

The server provides no mean for collaborators to list over projects it hosts. Exception is the server administrator who has, of course, access to everything. In general, however, one cannot access content without knowing a particular string. To decrease a chance of guessing other project's string, we advice to include long randomized sequence of characters (name obfuscation) into the string (Fiji plugins from this suite can do this for you). This is popular concept used in many online services.

The project on a server

Refer to this page to learn how projects are managed on the server.

The project inside Mastodon

There are four Fiji plugins to utilize the life cycle of a collaborative project.

Creating a new collaborative project

In this example, a project string = testProject is requested to be created on the server that is expected to be reachable on IP address 192.168.3.128 and port 7070. If the bottom toggle is checked, the secret project (its actual string will include random character sequence) is created on the server. The new project name should now be pre-filled in all plugins from this suite.

Contributing current snapshot

When creating a snapshot, it is always created locally in the same folder next to the main project file (the .mastodon file). Snapshot files use .mstdn extension. One is expected, however, to also upload a snapshot to the dedicated server. Make sure the toggle is checked to upload/report to the server as well.

To tell the content of snapshots apart, snapshot filenames are extended with any user text such as collaborator's name or name of the "isolated corner" of the tracked data. Please, avoid using "non-standard" characters and blank spaces. Moreover, the names of snapshots always include time stamps.

Here, a snapshot is created and consequently stored locally under the reported path. Since the "remote monitor" button is toggled, the snapshot file is also uploaded on the server into "testProject" folder.

Inspecting existing snapshots

When time is right, users might want to return to their previous work or inspect the current work of others within the same project. A plugin, whose control dialog is shown below, is available specifically for this task. This dialog collects a list of available snapshots first and user is expected to choose one and also choose what to do with it -- currently either to replace or merge with the current content in user's local Mastodon. Attention, plugin does not save anything before its operation, user has to do it herself (if she feels like...).

The snapshots are prefixed with one of three possible labels based on where they do exists:

• Local only: - stored previously but never contributed work of mine,
• Synced: - either already contributed work of mine, or previously downloaded work and now cached,
• Remote only: - not yet downloaded work of others.

User is choosing, in this example, to open certain synced snapshot (that will not be downloaded because it already exists locally) and to merge it with what is currently in his Mastodon session.

The content of the "Choose from the detected files" field is a result of inspection of the local folder and, since the checkbox is toggled, of the remote server (at the given address, port and from the given project).

The list shall be updated in response to updates of the input fields of the dialog. However, due to certain technical limits (of scijava automatic parameters harvesting), if the toggle button is changed, the dialog needs to be opened again (while its list is re-populated) to show the updated list. The previously opened dialog windows will be deprecated, that means, they will just close without doing anything when one clicks their "OK" or "Cancel" buttons.

Deleting old collaborative project

Finally, when all is done, contributed work is merged, overlaps are resolved, and .mastodon project is saved, one may want to remove the content on the server.

The dialog asks to delete a project folder "finishedCollaborativeProject" on the server. To prevent from unwanted effect of an accidental trigger of this menu, no deletion takes place until the "are you sure" toggle is checked.

Customizing the plugins

The plugins come with no predefined short-cuts but you can assign them shortcuts yourself the usual Mastodon way.

One can add own keyboard shortcuts from Mastodon main window, choose File -> Preferences..., choose the Keymap tab, then filter for "collab". To define a favourite shortcut, click on the action (e.g., "save current lineage"), click bottom to the field "Binding:" and type ctrl, hit space bar, T, hit space bar. To test it, which is to have the dialog pop up after pressing Ctrl+T, don't forget to click "Apply" in the dialog.