CREMI challenge EM Neuron Segmentation - BioImage.io

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

Updated: May 6

Author

Constantin Pape

Description

Neuron segmentation in EM, trained on the CREMI challenge data.

This model segments neurons in electron microscopy images. It predicts boundary maps segmenting neural membranes. The boundaries can be processed with Pixel Classifier to obtain an instance segmentation.

Input channel: EM grayscale image, 3D.
Scale: 4 nm per pixel, anisotropic (40 nm per pixel in z).
Bit depth: 8-bit
Output channel: cell membrane boundary maps probability.

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

Download

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Model file (.aiviadl)
Test image (.aivia.tif)

Download model file 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/.