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Last modified by annedevismes on 2021/06/08 11:56
From version 1.2
edited by puchades
on 2020/03/24 09:59
Change comment: There is no comment for this version
To version 7.1
edited by sharoncy
on 2020/03/28 14:59
Change comment: There is no comment for this version

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1 -XWiki.puchades
1 +XWiki.sharoncy
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1 -== H2 Headings Will Appear in Table of Content ==
1 +== [[image:ilastik_logo.PNG||style="float:right"]] ==
2 2  
3 3  
4 -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
4 +(% class="wikigeneratedid" %)
5 +== (% style="color:#c0392b" %)Analysis approach for series of rodent brain section image(%%) ==
5 5  
6 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
7 +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  
8 -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
9 +There are two main approaches for the analysis of rodent brain section images.
9 9  
10 -=== H3 Headings Will Appear In The Table of Content ===
11 +1. Pixel classification only (with two or more classes)
12 +1. Pixel classification with two classes (//immunoreactivity// and //background//), followed by object classification with two classes (//objects of interest// and //artefact//).
11 11  
12 -==== You can also add images ====
14 +**Which approach is best for my dataset?**
13 13  
14 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
16 +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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16 -Photo by David Clode
18 +=== (% style="color:#c0392b" %)Pixel classification workflow(%%) ===
17 17  
18 -==== Or code ====
20 +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]]
19 19  
20 -Code blocks can be added by using the code macro:
22 +**Basic steps:**
21 21  
22 -{{code language="python"}}
23 -x = 1
24 -if x == 1:
25 - # indented four spaces
26 - print("x is 1.")
27 -{{/code}}
24 +-Train the classifier with two classes (labeling and background)
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29 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30 -
26 +-Apply the classifier to the rest of the images (batch processing)
27 +
28 +-Export the probability maps in HDH5 format, and simple_segmentation images in PNG format with the default settings.
29 +
30 +-Review the results.
31 +
32 +=== (% style="color:#c0392b" %)Object classification workflow(%%) ===
33 +
34 +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//**.**
35 +
36 +-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.
37 +
38 +-In the **Input Data** applet, upload the original images and their respective probability maps in HDH5 format (output from the Pixel Classification).
39 +
40 +-Train the classifier with two classes (labelling and artefacts)
41 +
42 +(% class="wikigeneratedid" id="H" %)
43 +-In the **Object Information Export** applet, export “Object Predictions” in PNG format.  Do not change the default export location.
44 +
45 +(% class="wikigeneratedid" %)
46 +-Review the results.
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