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1	1	== [[image:ilastik_logo.PNG||style="float:right"]] ==
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3		-== (% style="color:#c0392b" %)Analysis approach for series of rodent brain section image(%%) ==
	3	+== [[image:Pixel_classification workflow.png||style="float:left"]](% style="color:#c0392b" %)Analysis approach for series of rodent brain section image(%%) ==
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5	5	Ilastik is a versatile image analysis tool specifically designed for the classification, segmentation and analysis of biological images based on supervised machine learning algorithms.
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7		-There are two main approaches for the analysis of rodent brain section images.
	7	+**There are two main approaches for the analysis of rodent brain section image**
8	8
9	9	1. Pixel classification only (with two or more classes)
10	10	1. Pixel classification with two classes (//immunoreactivity// and //background//), followed by object classification with two classes (//objects of interest// and //artefact//).
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24	24	* Export the probability maps in HDF5 format, and simple_segmentation images in PNG format with the default settings.
25	25	* Review the results.
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27		-[[image:Pixel_classification workflow.png||style="float:left"]]
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47	47	=== (% style="color:#c0392b" %)Object classification workflow(%%) ===
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49	49	There are three options on the ilastik start up page for running Object Classification.  Choose the //Object Classification with Raw Data and Pixel Prediction Maps as input//**.**
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53	53	* Train the classifier with two classes (labelling and artefacts)
54	54	* In the **Object Information Export** applet, export “Object Predictions” in PNG format.  Do not change the default export location.
55	55	* Review the results.
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