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GUIDE_QUICKSTART.md

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CellSketch quickstart commandline

Aim of this document

This guide will cover the basic steps to get from TIFF masks to a Blender rendering using the CellSketch components from the commandline.

Installation

We are using Album to run the different CellSketch components.

Install Album

Given that you already you already have a working conda / mamba / micromamba setup, run the following command:

conda create -n album album -c conda-forge

Alternative installation instructions are described here.

Activate the album environment before running the other commands in this guide:

conda activate album

Add the Helmholtz Imaging Development Catalog

album add-catalog https://github.com/betaseg/solutions

Install CellSketch solutions

Install these CellSketch solutions by running the following commands:

album install io.github.betaseg:cellsketch-create-project:0.2.2
album install io.github.betaseg:cellsketch-add-mask:0.2.1
album install io.github.betaseg:cellsketch-mesh-export:0.1.0
album install io.github.betaseg:cellsketch-to-blender:0.1.0
album install io.github.betaseg:launch-blender:0.1.0

Creating a CellSketch project

album run io.github.betaseg:cellsketch-create-project:0.2.2 --parent MY_PARENT_FOLDER --name MY_PROJECT --input MY_RAW_DATASET.tif --pixel_to_um 0.016 --headless True

Parameters:

  • parent: Choose a folder, let's call it MY_PARENT_FOLDER, where your project is going to be created in.
  • name: This name will represent your project, we will use the placeholder MY_PROJECT in this guide.
  • input: You need to provide one dataset as the source image, for example your raw dataset from the data acquisition. It will only be used for visualization purposes as the "background image", if you don't have one, you can simply choose one of your masks. You should be able to use any image file format that ImageJ / Fiji can open as well.
  • pixel_to_um: This is the conversion factor from pixel units to UM units.

A new folder MY_PARENT_FOLDER/MY_PROJECT.n5 will be created. Please don't rename it.

Add masks to the project

album run io.github.betaseg:cellsketch-add-mask:0.2.1 --project MY_PROJECT.n5 --input MY_MASK.tif --name mitochondria

Provide your MY_PROJECT.n5 directory from the previous step as the project input parameter and the mask you want to add as input, together with a representative name.

(Optional) Display project in BigDataViewer

Install the following solution:

album install io.github.betaseg:cellsketch-pixel-view:0.1.0

Now you can run the solution:

album run io.github.betaseg:cellsketch-pixel-view:0.1.0 --project MY_PROJECT.n5

The CellSketch Viewer

This will open BigDataViewer and initially always only display the source dataset. The view supports arbitrary rotations in 3D. Hover over the right part of the display - an arrow on the right border will appear. Click on it to show the sidebar of the viewer. After importing other cell components, they can be loaded and displayed by clicking on the eye symbols.

Exporting meshes for all masks

In order to render a cell in 3D, tools like Blender need mesh representations of your data. You can convert all or a subset of your masks and labels of your CellSketch project into meshes with one solution.

album run io.github.betaseg:cellsketch-mesh-export:0.1.0 --project MY_PROJECT.n5 --headless True

(Optional) Displaying meshes in VTK

Install the following solution:

album install io.github.betaseg:cellsketch-mesh-view:0.1.0

Run the solution:

album run io.github.betaseg:cellsketch-mesh-view:0.1.0 --project MY_PROJECT.n5

The CellSketch Viewer showing analysis results

Import meshes into Blender

All exported meshes can automatically be imported into Blender with the assigned colors to render them with advanced texture and lighting simulations.

album run io.github.betaseg:cellsketch-to-blender:0.1.0 --project MY_PROJECT.n5 --output_blend MY_PROJECT.blend --headless True

Parameters:

  • project: Your CellSketch project, the directory ending with .n5.
  • output_blend: The path to where the Blender project file will be stored, useful for further adjustments of the scene.
  • headless: This is set to False by default, which means the Blender scene will be displayed while importing the meshes. Be aware that the window will be frozen during this process. Set this to True to run the process in the background.

Open and render project in Blender

You can now open the Blender project stored at output_blend with Blender - either you already have Blender installed, then just open it there, or use the Album solution:

Run the following command:

album run io.github.betaseg:launch-blender:0.1.0 --input PATH_TO_OUTPUT_BLEND.blend

Rendering CellSketch meshes in Blender

The color of the material of each object can be changed in the Shading section in the lower part of the user interface. Adjustments to the rendering can be done after selecting the Rendering workspace in the top center area. Select Cycles in the right area as Render Engine for enhanced material rendering. GPU devices can be configured by clicking Preferences > System > Cycles Render Devices.

Click Render > Render image in the top menu to render the cell.

Alternatively, render the image via command line without displaying the Blender GUI with this call:

album run io.github.betaseg:launch-blender:0.1.0 --input PATH_TO_OUTPUT_BLEND.blend --output_rendering PATH_TO_OUTPUT_IMAGE

Rendering result