Input Files

It is recomanded to see the tutorial when using NeuroRetriever first time. (Tutorial page)
If your image is 3D TIF file, please use this tool(python) to convert it to AM format.



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Quick Start: Try your first NR segmentation!

1. Download the example AM file and SOMA file for your first test. The AM file is a gzipped raw image from confocal microscope in the AMIRA/AVIZO ASCII format. The SOMA file denotes the soma position of the neuron we want to segment from the raw image. The projection view of the raw image of this example file is shown in the figure below (grayscale image). The neuron of interest is denoted by the red square and the soma position is pointed by the red arrow. There are usually many neurons in the raw image (green arrows and texts), and gray background noise.

2. Click to upload these two files and then click the button from the user interface above. You will see the Job ID and the progress bar running.

3. After the job is done, you can find a green button. Click it and you will see this page:

They are the thumbnail of the segmented neuron with different HDR thresholding mask m. Smaller m keeps more detailed features of the neuron, but possibly noisier.

4. Choose the m value you want and click button. You will get the image file of the segmented single neuron.

5. For more details, please see the Tutorial page first for more detail.

After the segmentation done by NeuroRetriever, the single neuron image will be merged with the DLG channel image, traced the skeleton, warped into the standard brain, and archived into the FlyCircuit database, as in the figure below.