Platynereis EM Cells segmentation in EM - BioImage.io

jose-miguelserra-l
Jan 1, 2016
2 min read

Updated: May 7

Author

Constantin Pape

Description

These two models segment nuclei and cell boundaries respectively in electron microscopy images of Platynereis dumerilii (3D Stacks) from SBF-SEM. It predicts boundary maps and foreground probabilities. The boundaries can be processed e.g. with Cell Segmentation Recipe or Pixel classifier to obtain an instance segmentation (see also citation for segmentation algorithms)

Input channel: 3D images, grayscale
Scale: 4 nm/pixel in XY, 40 nm in Z
Bit depth: 8-bit
Output channel:
- For Nuclei: Channel 0, foreground probabilities, Channel 1: probability of boundary maps
- For Cells: Probability of boundary maps

This model was downloaded and converted from BioImage.io, respecting the associated license (see License section below for more information)

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Model files (.zip)
Test image (.tif)

Download model files and test image (ZIP archive)

Requirements

Make sure you have installed Aivia and the required DeepLearning module (according to our Wiki).

Installation and apply instructions

Aivia is required for applying the model file. You can request a demo copy of Aivia here.

Drag-and-drop the model file into the Recipe Console area; or use the 'Load recipe' option in the Recipe Console to load the model file.
Load the test image (or any image of your own) into Aivia.
If your image contains more than one channel, click on the 'Input & Output' section and specify the image channel you wish to apply the model on.
Click 'Start' to apply the model.

License

Acknowledgement

Bioimage.io is supported by AI4Life. AI4Life has received funding from the European Union's Horizon Europe research and innovation program under grant agreement number 101057970.

About AI4Life: https://ai4life.eurobioimaging.eu/.