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Getting Started

Setup LOST​

LOST releases are hosted on DockerHub and shipped in Containers. See quick-setup for more information.

Getting Data into LOST​

Image Data​

In the current version there is no GUI available in order to load images into LOST. So we will use the command line and a file explorer to do that. An image dataset in LOST is just a folder with images. LOST will recognize all folders that are located at path_to_lost/data/data/media in your filesystem, as it is mounted into the container. In order to add your dataset just copy it to the path below e.g.:

# Copy your dataset into the LOST media folder
cp -r path/to/my/dataset path_to_lost/data/data/media 

# It may be required that you copy it as a super user since the 
# docker container that executes LOST is running as root service 
# and owns the media folder.
sudo cp -r path/to/my/dataset path_to_lost/data/data/media

Then, if not already available, it is time to create a DataSource, with which you can then use a file browser and select your data, for a Pipeline to use. For the specifics, please refer to the Datasource page here.

LabelTrees​

Each LabelLeaf needs to have at least a name. Optional information for a LabelLeaf are a description, an abbreviation, an external ID (maybe from another system) and a color with which the label is displayed. LOST provides a GUI to create or edit LabelTrees and an import of LabelTrees defined in a CSV file via the command line or GUI. In order to be able to edit LabelTrees in LOST, you need to login as a user with role Designer. After login, you need to click the Labels button on the left navigation bar.

Users, Groups and Roles​

There are three roles in LOST: A Designer, an Annotator and an Admin role. All roles have different views and access to information. An Annotator's job is just to work on annotation tasks that are assigned to them, while a Designer may do more advanced stuff and everything an Annotator may do. For example a Designer will start annotation piplines and choose or edit LabelTrees for the annotation tasks. Lastly, an Admin is the most "powerful" role, as only these users can manage other users, groups and other things, which are integral parts of LOST.

Independent of their role, a user can be part of one or multiple user Groups. This way, annotation tasks can be a assigned to Groups of users that can work collaborative on the same task.

In order to manage users and groups, go to the Admin Area through the left menu bar. Please note that only users with the role Admin are allowed to access this part of LOST.

Starting an Annotation Pipeline​

Such a pipeline defines the order in which specific pipeline elements will be executed. Possible elements include Datasources, Scripts and AnnotationTasks.

Each version of LOST is equipped with a selection of standard pipelines that can be used as a quick start to annotate your data. In order to start an annotation pipeline you need to be logged in in as a user with role Designer and click on the Start Pipeline button on the left navigation bar. Now you will see a table with possible pipelines that can be started.

After selecting a pipeline by clicking on a specific row in the table, you need to configure it. A visualization of the selected pipeline will be displayed. In most cases, a Datasource is the first element of a pipeline. Click on it and select an available dataset. After a click on the OK button the pipeline element will turn green to indicate that the configuration was successful.

The next element you need to look for is an AnnotationTask. After clicking on it a wizard will pop up and guide you through the configuration of this AnnotationTask. In the first step, a name and instructions for the AnnotationTask can be defined. Click on the next button and select a user or group of users that should perform this AnnotationTask. Now a LabelTree need to be selected by clicking on a specific tree in the table. Now a visualization of the LabelTree will be displayed. Here you can select a subset of labels that should be used for the AnnotationTask. The idea is that each parent leaf represents a category that can be selected to use all direct child leafs as labels. So if you click on a leaf, all direct child leafs will be used as possible labels for the AnnotationTask. It is possible to select multiple leafs as label categories and then proceed. After configuring the last of these tabs, click on OK and the configuration of this AnnotationTask is done.

Now visit all other pipeline elements that have not been configured (indicated by a yellow color) and move on to the next step in the wizard, by clicking "Next". In the upper right corner of the screen. Here you have to enter a name and a description of your pipeline. After entering these informations you can click on the checkmark symbol to get to the Start Pipe button. With a click on this button your annotation pipeline will be started, good job.

You can monitor the state of all running pipelines by clicking on the Pipelines button in the left navigation bar.

To get to a specific pipeline, click on the inspect pipelines with the eye-symbol in the row of the according pipeline in the table.

For a simple start, use the minimal mia and sia pipelines, according to your needs. Should you already have annotations in LOST format, you can reannotate them with the mia_request_again and sia_request_again pipeline templates.

Annotating Images​

After the AnnotationTask has been created by the pipeline, the selected annotators will be able to work on it. The tasks are available under the point Annotation, you can see in the navigation bar on the left. If you are logged in as a user with role Annotator you see this directly after login.

Here you can see a table with all available AnnotationTasks for you. Click on the Annotate button in the row of a taks you want to work on and you will be redirected to one of the annotation tools (see also the annotators chapter). Now instructions will pop up and you are ready to annotate.

Downloading Annotation Results​

Exports can be done either by GUI or the API.

Export Per GUI​

The tradtional way to export annotations is by using the GUI. This provides two ways to export the data, one of them being by going to the Pipeline the AnnotationTask was created in, like described above, in the Starting an Annotation Pipeline section. There, when inspecting the according pipeline, you can select the AnnotationTask. In the first tab of the now opened window, Generate Export, you can first generate an export. Then, in the tab right next to it, Available Exports, you can download all created exports of this AnnotationTask.

To export the data of a whole Dataset or a single AnnootationTask within one, go to the Datasets page, reachable through the navigation bar. There, select the button with "export datasets" Here are Buttons to first generate new exports and then to download them.

Export Per API​

For automated exports or otherwise exporting by using the API, please refer to the API documentation under <Adress-of-the-LOST-Service>/api.