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1	1	== [[image:ilastik_logo.PNG||style="float:right"]] ==
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3		-== [[image:Pixel_classification workflow.png||style="float:left"]](% style="color:#c0392b" %)Analysis approach for series of rodent brain section image(%%) ==
	3	+== (% 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.
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18		-There are two main approaches for the analysis of rodent brain section image
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20	20	1. Pixel classification only (with two or more classes)
21	21	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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35	35	* Export the probability maps in HDF5 format, and simple_segmentation images in PNG format with the default settings.
36	36	* Review the results.
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	27	+[[image:Pixel_classification workflow.png||style="float:left"]]
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56	56	=== (% style="color:#c0392b" %)Object classification workflow(%%) ===
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58	58	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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62	62	* Train the classifier with two classes (labelling and artefacts)
63	63	* In the **Object Information Export** applet, export “Object Predictions” in PNG format.  Do not change the default export location.
64	64	* Review the results.
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