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Last modified by annedevismes on 2021/06/08 11:56
From version 10.1
edited by puchades
on 2020/04/07 16:43
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 -XWiki.puchades
1 +XWiki.evanhancock
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15 15  
16 16  === (% style="color:#c0392b" %)Pixel classification workflow(%%) ===
17 17  
18 -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]].
19 19  
20 20  **Basic steps:**
21 21  
22 --Train the classifier with two classes (labeling and background)
22 +* Train the classifier with two classes (labeling 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.
23 23  
24 --Apply the classifier to the rest of the images (batch processing)
25 -
26 --Export the probability maps in HDF5 format, and simple_segmentation images in PNG format with the default settings.
27 -
28 --Review the results.
29 -
30 30  === (% style="color:#c0392b" %)Object classification workflow(%%) ===
31 31  
32 32  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//**.**
33 33  
34 --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.
35 -
36 --In the **Input Data** applet, upload the original images and their respective probability maps in HDF5 format (output from the Pixel Classification).
37 -
38 --Train the classifier with two classes (labelling and artefacts)
39 -
40 -(% class="wikigeneratedid" id="H" %)
41 --In the **Object Information Export** applet, export “Object Predictions” in PNG format.  Do not change the default export location.
42 -
43 -(% class="wikigeneratedid" %)
44 --Review the results.
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.