Automated three-dimensional detection and counting of neuron somata.
J Neurosci Methods
; 180(1): 147-60, 2009 May 30.
Article
in En
| MEDLINE
| ID: mdl-19427542
ABSTRACT
We present a novel approach for automated detection of neuron somata. A three-step processing pipeline is described on the example of confocal image stacks of NeuN-stained neurons from rat somato-sensory cortex. It results in a set of position landmarks, representing the midpoints of all neuron somata. In the first step, foreground and background pixels are identified, resulting in a binary image. It is based on local thresholding and compensates for imaging and staining artifacts. Once this pre-processing guarantees a standard image quality, clusters of touching neurons are separated in the second step, using a marker-based watershed approach. A model-based algorithm completes the pipeline. It assumes a dominant neuron population with Gaussian distributed volumes within one microscopic field of view. Remaining larger objects are hence split or treated as a second neuron type. A variation of the processing pipeline is presented, showing that our method can also be used for co-localization of neurons in multi-channel images. As an example, we process 2-channel stacks of NeuN-stained somata, labeling all neurons, counterstained with GAD67, labeling GABAergic interneurons, using an adapted pre-processing step for the second channel. The automatically generated landmark sets are compared to manually placed counterparts. A comparison yields that the deviation in landmark position is negligible and that the difference between the numbers of manually and automatically counted neurons is less than 4%. In consequence, this novel approach for neuron counting is a reliable and objective alternative to manual detection.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Pattern Recognition, Automated
/
Cell Count
/
Microscopy, Confocal
/
Imaging, Three-Dimensional
/
Nervous System
/
Neurons
Type of study:
Diagnostic_studies
Limits:
Animals
Language:
En
Journal:
J Neurosci Methods
Year:
2009
Document type:
Article
Affiliation country:
Germany