Last modified by annedevismes on 2021/06/08 11:56
From version 15.1
edited by puchades
on 2020/09/24 12:15
Change comment: There is no comment for this version
To version 11.1
edited by evanhancock
on 2020/07/21 09:34
Change comment: There is no comment for this version

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1 1  == [[image:ilastik_logo.PNG||style="float:right"]] ==
2 2  
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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20 -There are two main approaches for the analysis of rodent brain section image
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22 22  1. Pixel classification only (with two or more classes)
23 23  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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25 25  **Which approach is best for my dataset?**
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27 -As a general rule, pixel classification is suitable for images in which there are clear differences in the colour, intensity and / or texture of the feature of interest (labelling) versus the background and other structures.  If there is non-specific labelling in the image that is very similar in appearance to the labelling of interest, object classification may allow the non-specific labelling to be filtered out based on object level features such as shape and size. The best approach is determined by trial and error.
14 +As a general rule, pixel classification is suitable for images in which there are clear differences in the colour, intensity and/ or texture of the feature of interest (labelling) versus the background and other structures.  If there is non-specific labelling in the image that is very similar in appearance to the labelling of interest, object classification may allow the non-specific labelling to be filtered out based on object level features such as size and shape. The best approach is determined by trial and error.
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29 29  === (% style="color:#c0392b" %)Pixel classification workflow(%%) ===
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33 33  **Basic steps:**
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35 -* Train the classifier with two classes (labelling and background)
22 +* Train the classifier with two classes (labeling and background)
36 36  * Apply the classifier to the rest of the images (batch processing)
37 37  * Export the probability maps in HDF5 format, and simple_segmentation images in PNG format with the default settings.
38 38  * Review the results.
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58 58  === (% style="color:#c0392b" %)Object classification workflow(%%) ===
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60 60  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//**.**
Pixel_classification workflow.png
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