Using Organelle Morphology¶

Marimo GUI¶

Organelle Morphology comes with a graphical interface which runs in the browser and is produced by marimo.

Make sure your conda environment is active and run:

marimo run notebooks/ui.py

Organelle Morphology should open in a new browser tab.

Walkthrough¶

Lets go one by one from left to right, from top to bottom through the available panels in OM.

Create a project¶

A project is a directory where OM can save data to. It can contain the microscopy data belonging to this project. OM will write analysis outputs and its cache to the project directory.

In the UI, to select a directory make sure to click on the folder icon! Create the project by clicking Load Project.

Loading Sources¶

OM works with three dimensional segmentations of microscopy images. Currently, OM can only handle outputs from CebraEM in the n5 format. CebraEM stores the actual data in the .n5 file and creates an additional .xml file in the same directory as the n5.

To load an image, in the Add Source panel, navigate to the directory containing your data. Select one xml file and type the name you want to give the corresponding type of organelle below, then click Load Source.

Repeat until you have all sources loaded you need.

You can see the currently loaded sources below the loading panel.

Having sources loaded activates most other functionality in the app.

Compression and Clipping¶

To make computations faster and previewing more practical, OM allows to crop the data and not load everything. This is called clipping and works by defining the lowest corner and the highest corner of a cube. Everything outside is not loaded. Make sure to activate the switch if you want to clip your data.

If your data comes with multiple compression levels, you can select here on which one you'd like to work. s3 is the corresponds to the lowest resolution, s0 is full resolution.

OM computes meshes from the given segmentations. These meshes are by default very dense, they have a constant density of one vertex per voxel. You can choose to simplify the mesh by a percent value, removing this amount of vertices from each mesh.

Mesh simplification can significantly speed up most computations in OM, but it also introduces a bit of error, especially to area computations.

Progress¶

Here the progress of jobs running in the parallelization backend are shown. You can open the dashboard to see more information (only clickable while the app is idle).

Load Analysis Records¶

When the Project contains some analysis records from a previous run, you can load them here.

Show Mesh¶

Here you can preview the mesh in 3D. By default the meshes are colored by organelle type.

• Organelle id filter: filter what is displayed. * can be any text. Separate multiple filters with a comma.
• Highlight ids: Choose which ids to highlight. Makes everything else gray. If empty, the color is unchanged
• Skeleton: Display the skeleton, if computed. Make sure to activate High-quality viewer to make the mesh transparent.
• Curvature: Color the mesh by its local curvature.
• Color individual organelles: Each organelle instance is colored differently.
• MCS: Membrane contact site. See below for an explanation of all options.
• Box settings: Draw a box to help decide on clipping settings for higher resolution levels. Also used in Get IDs of organelles in box
• Min volume: Color by a minimum volume. Everything smaller is orange, all bigger organelles are green. Meshes with openings are displayed gray. Does not work with other coloring options in parallel.
• Show rotation: Display two lines indicating a rotation by a given angle. Yellow is the reference 0° line, orange is the rotated line.
• High-quality viewer: Opens the view in a separate window with better quality. (Transparency only works here)

Additional to the meshes, the chosen clipping box is shown, as well as an box enclosing the unclipped data.

The (0,0,0) corner is marked with three arrows along the axes. The red one points in x direction, the green one in y direction and the blue one in z direction.

Set minimum Volume¶

Remove organelles below a certain volume from all calculations, including the 3D rendering. Use the option in Show Mesh to preview your selection.

Cache¶

Display the contents of the project cache or clean it.

Skeletonize¶

Calculate a skeleton for the selected organelles.

For information about the algorithms and options see the skeletor documentation

Membrane Contact Sites (MCS)¶

Calculate sites where two meshes are close. Choose an upper and lower distance threshold to define what counts as a contact. Then select between which groups of organelles to search for contacts.

You could set Labels 1 to er_* and Labels 2 to * to find all contacts with at least one er organelle involved. er_0001 and mito_* would find all contacts between the er_0001 organelle and any mito organelle.

Position Analysis¶

Create 2d or 1d histograms of organelle densities. In contrast to most analysis, this one works not with the mesh data, but with the raw volume. The compression setting is still respected.

First you have to choose which organelle type to consider. Then select the bin size, choosing a higher bin size can speed up the calculations.

Select whether you want a 2d or 1d histogram. For 2d you can select which axis to collapse, for 1d you can select the axis which you want to retain.

Before running the calculations, you can rotate the 3d volume if necessary to align it better to other data.

Analysis Records¶

Running analysis generates records of these analysis. They contain the measurements and metadata of the settings how they were generated, as well as metadata about the sources and project.

Here you see an overview of all currently loaded records, and you can save them to the project folder.

2D Profile Calculations¶

Analyse the shape of organelles by looking at 2d cross-sections.

• Fixed Axis cuts perpendicular to a chosen axis
• Random Planes cuts using randomly generated planes
• Skeleton cuts perpendicular to a skeleton. The skeleton needs to be generated already!