MoBIE

MultiModal Big Image Data Sharing and Exploration

Exploring segmentations

Adding a segmentation to the viewer, will display it as a coloured overlay on your image. If available, a corresponding table will also appear, where each row corresponds to one segmented object.

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Both the table and segmentation overlay can be explored interactively:

Interacting with the segmentation in the viewer

All keyboard shortcuts are available by clicking Help > Show Segmentation Image Help in the menu at the top of the table.

To summarise:

More options are available if you right click in the viewer: image

Interacting with segmentation table

Clicking on a row in the table, will move you to the location of that object in the viewer. Ctrl + clicking on a row, will also select that object.
The first column ‘label_id’ states the id of each segmented object from the image.

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Adding more tables

Usually, the default table that appears with a segmentation only contains very minimal information e.g. the position of objects and their bounding boxes.

You can add more tables from the project, by selecting Table > Load Columns… and then Load columns From Project. This will make a dropdown menu appear with all available tables. e.g. in the example Platybrowser project there are tables for morphology statistics, gene expression and more…

New columns will be added to the right of table, and can be viewed by scrolling horizontally on the bar at the bottom of the table.

You can also add tables from your File System (see tutorial here)

Colour by column…

Selecting Color > Color By Column… from the table menu will allow you to colour your segmented objects based on the values in a certain column. e.g. you could colour based on the value of a calculated statistic, or based on membership to different clusters.

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The dialog allows you to select the Column you want to colour based on, and a colouring mode. The final checkbox Paint Zero Transparent controls whether 0 values are transparent in the viewer or not.

Colouring Modes:

For the palettes designed for numerical data, a popup will appear allowing you to change the minimum and maximum values for the colour palette. This is useful if you want to focus on / see differences in a smaller range of values.

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Saving tables

Tables can be saved by using Table > Save Table as… in the menu at the top of the table.

Specific columns can be saved by using Table > Save Columns as…

They will be saved as tab separated files.