Interface Overview

Here we provide an overview of the LimbNET client interface, available options and general functionality in the different task views.

Welcome view, and main window

Upon opening LimbNET, the first thing you will normally see is the welcome view.

This view provides a brief overview of the LimbNET client, and allows you to navigate to the other functional views:

Welcome view and main window of the LimbNET client. — The welcome view, and main window, of the LimbNET client.

As seen in the figure above, the main window of the LimbNET client is arranged as follows:

The header bar at the top of the window, where (a) the main menu can be opened/closed, and (b) auxiliary client options are available (left to right):
- Open documentation
- Contact the LimbNET team
- Information
- User information
- Logout
The main menu on the left side of the window - a navigation bar - which allows you to navigate between the core data views, described in further detail below.
The main viewport on the right side of the window, which displays the currently selected view.
The status bar which shows the current connection status to the LimbNET server.

In the figure above, the main view is occupied by the welcome message, since we have begun at the home screen. Below we provide a high level overview of the other view types.

Task and data views

The data views accessible from the main navigation menu are all fundamentally data listings (tables) of the available data for each data type. The order of data types, from top to bottom, loosely resembles a possible typical workflow or pipeline: from sets of raw images, through digitisation and spatiotemporal sequences, to models and simulations.

Note

The core high level data views - raw images, staged images, single frame patterns, molecular field sequences, models - all share a similar tabular structure.

From each of the listing views, some high-level data manipulation options are available, and for each data type a data-specific editor view can also be opened. The data-specific editors generally include more options, or as in the case of the model editor, for example, a complete interface for a specific task.

Info

While we provide a high-level overview in this section, more detailed information about each view is available in the user guide.

General structure

We first introduce the general structure of the tabular data views, using the images view as an illustrative example.

On the left, in the navigation menu, the currently open view is highlighted.

The main viewport shows a typical data table view of all raw image data available to the current user, in a tabulated format. Each individual available dataset occupies a data row.

Above the data table are a set of filters which allow the user to control search and filtering criteria for the current data type. For example, it is common to filter by the name of a dataset, or a tag that has been applied (e.g., a gene).

The options available for each data row will vary according to the type of data/view, and are detailed further in the relevant section(s). The options section of a data row will generally have the same structure across data types, with some shared common controls, followed by data-specific controls.

Options common to all data

Some per-data row options are common across all types of data. Here we can see, from left to right:

A switch that controls data visibility (public/private).
Delete data item button.
Open the editor for this data row.
Data-specific options (in this case, "stage", i.e. open the image data in the staging view).

Note

Some options may only be available to the owner of that data item.

The table can be sorted, according to a subset of the available headers/fields (e.g., image name, owner's username, etc.). The pagination controls at the bottom allow the user to select the number of items per page for a given search, a summary of the number of items in the database for the current search criteria, and navigation buttons.

Finally, where a data type can be filtered by tags, and there is a column that displays the tag(s), clicking on a tag in the relevant column will add that tag to the search criteria; if a tag is selected, then clicking it again will remove it from the search criteria.

Navigable preview

For some data types, e.g., images, stagings, digitisations and molecular field sequences data items can be previewed without navigating away from the table view. In these data views, clicking on a data item (name, thumbnail, ...) will open up a preview window as in the image below.

The window will show a preview of the current data item, including any relevant controls (e.g., time slider in the case of molecular field sequences).

Other common preview functionality consists of the following:

Data title.
Close preview button (return to the table).
Data-specific manipulations - some may only be enabled if you're the owner of the data.
Previous item; this will navigate to the previous item in the table corresponding to the current search criteria, and open it directly in the current preview window. If no item is available, the button will be disabled.
Next item. As per (4.) above, but will navigate forwards through items in the current search.

Specific data views

Raw images

The first data type available in the interface are raw images of gene expression patterns in mouse embryonic limb buds. These may correspond to in-situ hybridisation gene expression, fluorescence, etc.

A navigable preview of the current image search can be opened by clicking on the thumbnail or the image name.

New images can be uploaded by clicking "upload image" and following the associated dialog.

Filters

The table can be filtered according to the following criteria:

Image name; case-insensitive, matches words present in the image title.
Gene tag; matches images that have an associated tag, scroll the list or start typing a gene name to filter the list of tags.
Staging; whether the image has been staged, or not.
Mine; show only the images that belong to the current user, or all images.

Image data and options

Each data item permits the following options, for the data owner:

Change public/private status (switch),
Delete image,
Open image editor.

All users can open the Staging view for a given image.

Staged images

Raw images - of mouse embryonic limb buds - can be staged using the staging tool, accessed from the images listing, or the image editor.

Once staged, the images will be normalised: they will be rotated so that the region containing the limb bud is always in the same orientation, and cropped to the region closely surrounding the limb bud. All images processed in this way can be seen in this view.

Staged/normalised image data listing overview.

A navigable preview of the current search can be opened by clicking on the thumbnail or the staged image name.

Filters

The table can be filtered according to the following criteria:

Staged image name; case-insensitive, matches words present in the staged image title.
Gene tag; matches stagings whose parent image has an associated tag, scroll the list or start typing a gene name to filter the list of tags.
Filter by side; whether the staging system has detected the limb as being on the left or right side of the embryo.
Mine; show only the stagings that belong to the current user, or all images.

Tip

The staged images can be sorted by the staged time point. So, a nice technique for getting a basic overview of the behaviour of a particular gene over time is to filter the gene tag of interest, sort by staging time, and scroll through the navigable preview images.

Staged image data and options

Each data item permits the following options, for the data owner:

Change public/private status (switch).

All users can open the Staging view for a given staged image, in order to modify the staging of that image.

Single frame patterns

Once an image has been staged and normalised, it can be digitised into a single frame pattern. This process maps the intensity values derived from the raw image data into a mesh, corresponding to the geometry of a morphomovie at the staged time point.

As with stagings, single frame patterns can also be sorted by time point.

For any given single frame pattern, a navigable preview of the current search can be opened by clicking on the name of the single frame pattern data. This will open a navigable preview which shows both the staged image and the corresponding digitised pattern at the same time.

Filters

The table can be filtered according to the following criteria:

Pattern name; case-insensitive, matches words present in the pattern title.
Gene tag; matches patterns whose parent image has an associated tag, scroll the list or start typing a gene name to filter the list of tags.
Filter by time; show only patterns that correspond to a single staged time point.
Digitisation only; show only the patterns that are a direct output of the digitisation process, and are not derived (i.e., edited in some further way).
MFS; show only patterns that are associated with some molecular field sequence (will generally show nothing if only direct digitisations are enabled).
Morphomovie; show only patterns that are associated with a specific morphomovie (shape), i.e., mouse limb, square, etc.

Single frame pattern data and options

Each data item permits the following options, for the data owner:

Change public/private status (switch),
Delete the digitisation.

All users can open the Staging/Digitisation view for a given pattern, as well as the underlying image properties. Additionally, all users can open the pattern editor for a given pattern, by clicking Edit.

Molecular field sequences

Molecular field sequences (MFS) consist of a series of patterns (digitised, or from simulation) changing over time with the changing 2D morphomovie.

For the time being, the functionality related to MFS is restricted, however this is due to change soon as we implement new functionality for quickly and easily creating your own MFS.

Molecular field sequence listing overview.

For any given MFS, a navigable preview of the current search can be opened by clicking on the name of the MFS data. This will open a preview of the full morphomovie for the selected MFS, that can be played back and viewed at any valid point in time.

Tip

Looking for a specific molecular sequence, or sequences, to use in a model? With the model editor open, open the MFS listing in a separate tab. Now you can search and filter all MFS of interest without having to leave the model editor, and review each one's full data set.

Filters

The table can be filtered according to the following criteria:

MFS name; case-insensitive, matches words present in the MFS title.
Gene tag; matches MFSs with an associated tag, scroll the list or start typing a gene name to filter the list of tags.
Morphomovie; show only MFSs that are associated with a specific morphomovie (shape), i.e., mouse limb, square, etc.

Molecular field sequence data and options

Each data item permits the following options, for the data owner:

Change public/private status (switch).

Models

All models that belong to the current user, or are public, can be viewed in a data table view similar to all the other data in LimbNET.

Note

The models listing is slightly different to the others as clicking on a model will directly open the editor for that model specification, rather than an inline preview.

Tip

Looking for demos or tutorials of LimbNET's functionality? Filter by the demo tag to see some pre-made examples.

It is possible to create a new model from the models listing at any point, by clicking the New model button in the top right.

For any given model, a preview of the detailed description of that model (if the owner has provided one) can be opened by clicking the small arrow on the left side of the corresponding row.

Filters

The table can be filtered according to the following criteria:

Model name; case-insensitive, matches words present in the model title.
Gene tag; matches models with an associated gene tag, scroll the list or start typing a gene name to filter the list of tags.
Model tag; matches models with an associated model tag (demo, publication, ...), scroll the list or start typing a gene name to filter the list of tags.
Mine; show only the models that belong to the current user, or all models.

Model data and options

The model owner can change public/private status (switch), of any model that they own. They can also delete their own models.

All users can open the Simulation view for any visible model, that belongs to them, or any public model, by clicking the Sim button corresponding to that model.