Changes for page ilastik

Last modified by abonard on 2025/04/10 15:14
From version 2.1
edited by jessicamitchell
on 2023/09/11 11:44
Change comment: There is no comment for this version
To version 20.1
edited by abonard
on 2025/04/10 15:14
Change comment: There is no comment for this version

Summary

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Author
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1 -XWiki.jessicamitchell
1 +XWiki.abonard
Content
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1 -Available tutorials:
2 2  
3 -=== [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel=" noopener noreferrer" target="_blank"]] ===
4 4  
5 -//Level: advanced//
3 +* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
6 6  
7 -Boundary-based segmentation with Multicut
5 +* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
6 +
7 +=== **Beginner** ===
8 +
9 +=== [[QUINT Workflow – Atlas-based quantification and spatial analysis>>https://www.youtube.com/watch?v=n-gQigcGMJ0||rel=" noopener noreferrer" target="_blank"]] ===
10 +
11 +**Level**: beginner(%%) **Type**: video tutorial
12 +
8 8  {{html}}
9 -<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/leuTtIAmEwE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
14 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/n-gQigcGMJ0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
10 10  {{/html}}
11 -=== [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel=" noopener noreferrer" target="_blank"]] ===
16 +=== **Advanced** ===
12 12  
13 -//Level: advanced//
18 +=== [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel=" noopener noreferrer" target="_blank"]] ===
14 14  
20 +**Level**: advanced(%%) **Type**: video tutorial
21 +
22 +Learn how to use the object classification workflow to classify full objects, based on object-level features and user annotations.
15 15  {{html}}
16 -<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/xGyTriPQXHI" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
24 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/SQeRGvHeT3o" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
17 17  {{/html}}
18 -=== [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel=" noopener noreferrer" target="_blank"]] ===
26 +=== [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel=" noopener noreferrer" target="_blank"]] ===
19 19  
20 -//Level: advanced//
28 +**Level**: advanced(%%) **Type**: video tutorial
21 21  
30 +This demonstration guides you through the Pixel Classification workflow by showing you how to assign labels to pixels based on pixel features and user annotations. Showing you how to select features of generic pixel features, smoothed pixel intensity, edge filters and texture descriptors.
22 22  {{html}}
23 -<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/N-QhiTWVDmk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
32 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/5N0XYW9gRZY" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
24 24  {{/html}}
25 25  === [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel=" noopener noreferrer" target="_blank"]] ===
26 26  
27 -//Level: advanced//
36 +**Level**: advanced(%%) **Type**: video tutorial
28 28  
29 29  {{html}}
30 30  <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/n-gQigcGMJ0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
31 31  {{/html}}
32 -=== [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel=" noopener noreferrer" target="_blank"]] ===
41 +=== [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel=" noopener noreferrer" target="_blank"]] ===
33 33  
34 -//Level: advanced//
43 +**Level**: advanced(%%) **Type**: video tutorial
35 35  
36 -Object classification
45 +This demo will guide you through the different types of tracking workflows in ilastik.
37 37  {{html}}
38 -<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/SQeRGvHeT3o" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
47 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/bZoWx2FuT08" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
39 39  {{/html}}
40 -=== [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel=" noopener noreferrer" target="_blank"]] ===
49 +=== [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel=" noopener noreferrer" target="_blank"]] ===
41 41  
42 -//Level: advanced//
51 +**Level**: advanced(%%) **Type**: video tutorial
43 43  
53 +In this demo we want to briefly show you how you can use the carving module to aid you in the extraction of objects from images that are only separable by their boundary - i.e. objects that do not differ from the rest of the image by their internal appearance.
44 44  {{html}}
45 -<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/5N0XYW9gRZY" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
55 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/xGyTriPQXHI" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
46 46  {{/html}}
57 +=== [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel=" noopener noreferrer" target="_blank"]] ===
58 +
59 +**Level**: advanced(%%) **Type**: video tutorial
60 +
61 +In this workflow we will look into how to add dots for the object instances, brush strokes over the background
62 +and add boxes to monitor the count in sub-image regions.
63 +{{html}}
64 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/N-QhiTWVDmk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
65 +{{/html}}
47 47  === [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel=" noopener noreferrer" target="_blank"]] ===
48 48  
49 -//Level: advanced//
68 +**Level**: advanced(%%) **Type**: video tutorial
50 50  
70 +This short video demonstrates how to export ilastik tracking results for visualization/proofreading to MaMuT.
51 51  {{html}}
52 52  <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/kjVqWSSdDmU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
53 53  {{/html}}
54 -=== [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel=" noopener noreferrer" target="_blank"]] ===
74 +=== [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel=" noopener noreferrer" target="_blank"]] ===
55 55  
56 -//Level: advanced//
76 +**Level**: advanced(%%) **Type**: video tutorial
57 57  
78 +This tutorial will guide you through the boundary-based segmentation with Multicut.
58 58  {{html}}
59 -<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/bZoWx2FuT08" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
80 +<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/leuTtIAmEwE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
60 60  {{/html}}
61 61