AutoNeuron Step 3: Soma detection

AutoNeuron detects somas based on their relative contrasts and size constraints:

• A lower value generally yields larger somas.
• A higher value generally yields smaller somas.

Use the slider or type a value.

The default value is the value entered previously for the maximum process parameter.

To change the value:

• Type a value

OR

• Click Measure in Image and measure a soma:
  1. Click just outside one of the outer edges of the soma to place the start point.
  2. Click opposite the start point, just outside the outer edge of the soma, to place the end point.

• Click Find All.

AutoNeuron identifies all the somas that meet your criteria.

When complete, AutoNeuron displays the number of somas detected.

If this is not satisfactory:

1. Click Clear to remove all detected somas.
2. Use the slider to adjust the Soma Detector Sensitivity.
3. Modify the minimum soma size under Ignore Somas Smaller Than.
4. Click Redetect Somas.

AutoNeuron clears the previously detected somas and finds those matching your new settings.

5. When you are satisfied with the results, click Next Step.