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Last modified by annedevismes on 2021/06/08 11:56
From version 2.3
edited by puchades
on 2020/03/25 14:56
Change comment: There is no comment for this version
To version 20.2
edited by annedevismes
on 2021/06/08 10:57
Change comment: There is no comment for this version

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1 -== Analysis approach for series of rodent brain section image ==
1 +== [[image:ilastik_logo.PNG||style="float:right"]] ==
2 2  
3 -There are two main approaches for the analysis of rodent brain section images.
3 +== [[image:Pixel_classification workflow.png||style="float:left"]](% style="color:#c0392b" %)Analysis approach for series of rodent-brain section image(%%) ==
4 4  
5 -1. Pixel classification only (with two or more classes)
6 -1. Pixel classification with two classes (//immunoreactivity// and //background//), followed by object classification with two classes (//objects-of-interest// and //artefact//).
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.
7 7  
7 +**There are two main approaches for the analysis of rodent-brain section image~:**
8 +
9 +1. pixel classification only (with two or more classes) and
10 +1. pixel classification with two classes (//immunoreactivity// and //background//), followed by Object classification with two classes (//objects of interest// and //artefact//).
11 +
8 8  **Which approach is best for my dataset?**
9 9  
10 -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 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.
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 on the basis of the object-level features such as shape and size. The best approach is determined by trial and error.
11 11  
12 -=== Pixel classification workflow ===
16 +=== (% style="color:#c0392b" %)Pixel classification workflow(%%) ===
13 13  
14 -For a quick introduction, watch: [[https:~~/~~/www.youtube.com/watch?v=5N0XYW9gRZY&feature=youtu.be>>url:https://www.youtube.com/watch?v=5N0XYW9gRZY&feature=youtu.be]]
18 +For a quick introduction, [[watch this video>>https://www.youtube.com/watch?v=5N0XYW9gRZY&feature=youtu.be]].
15 15  
16 -=== Object classification workflow ===
20 +**Basic steps**
17 17  
22 +* Train the classifier with two classes (labelling and background).
23 +* Apply the classifier to the rest of the images (batch processing).
24 +* Export the probability maps in HDF5 format and simple_segmentation images in PNG format with the default settings.
25 +* Review the results.
18 18  
19 -==== ====
27 +=== (% style="color:#c0392b" %)Object-classification workflow(%%) ===
20 20  
29 +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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22 -
31 +* Save the object-classification file in the same folder as the raw images for analysis. If the images are moved after the //ilastik// file is created, the link between the //ilastik //file and the images may be lost, resulting in a corrupted file.
32 +* In the "Input Data" applet, upload the original images and their respective probability maps in HDF5 format (output from the Pixel Classification).
33 +* Train the classifier with two classes (labelling and artefacts).
34 +* In the "Object Information Export" applet, export “Object Predictions” in PNG format.  Do not change the default export location.
35 +* Review the results.
Pixel_classification workflow.png
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