Last modified by puchades on 2022/09/30 16:01
From version 21.1
edited by tomazvieira
on 2022/01/25 19:18
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To version 25.1
edited by puchades
on 2022/02/15 09:16
Change comment: There is no comment for this version

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1 -== What is webilastik? ==
1 +== What is Webilastik? ==
2 2  
3 3  
4 4  Classic [[ilastik>>https://www.ilastik.org/]] is a simple, user-friendly desktop tool for **interactive image classification, segmentation and analysis**. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed **lazily**, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.
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5 5  
6 6  [[webilastik>>https://app.ilastik.org/]] is a web version of ilastik's Pixel Classification Workflow, integrated with the ebrains ecosystem. It can access the data-proxy buckets for reading and writing (though reading is still suffering from latency issues). It uses Neuroglancer as a 3D viewer as well as compute sessions allocated from the CSCS infrastructure.
7 7  
8 -== How to use webilastik ==
8 +== How to use Webilastik ==
9 9  
10 10  === Opening a sample Dataset ===
11 11  
12 -Go to [[app.ilastik.org>>app.ilastik.org/]] and load a [[Neuroglancer Precomputed Chunks dataset>>https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed]]. You can e.g. use a sample data set that is already in the server by pasting the following URL into Neuroglancer's prompt:
12 +Go to [[https:~~/~~/app.ilastik.org/>>https://app.ilastik.org/]] and load a [[Neuroglancer Precomputed Chunks dataset>>https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed]]. You can e.g. use a sample data set that is already in the server by pasting the following URL into Neuroglancer's prompt:
13 13  
14 14  precomputed:~/~/https:~/~/app.ilastik.org/public/images/c_cells_2.precomputed
15 15  
16 16  [[image:image-20220125164204-2.png]]
17 17  
18 +
19 +=== Opening a Dataset from the data-proxy ===
20 +
21 +You can also load Neuroglancer Precomputed Chunks data from the data-proxy; The URLs for this kind of data follow the following scheme:
22 +\\##precomputed:~/~/https:~/~/data-proxy.ebrains.eu/api/buckets/(% style="background-color:#3498db; color:#ffffff" %)my-bucket-name(% style="background-color:#9b59b6; color:#ffffff" %)/path/inside/your/bucket(%%)##
23 +
24 +So, for example, to load the sample data inside the (% style="background-color:#3498db; color:#ffffff" %)quint-demo(%%) bucket, under the path (% style="background-color:#9b59b6; color:#ffffff" %)tg-ArcSwe_mice_precomputed/hbp-00138_122_381_423_s001.precomputed(% style="color:#000000" %) (%%) like in the example below:
25 +
26 +
27 +[[image:image-20220128142757-1.png]]
28 +
29 +=== ===
30 +
31 +you would type a URL like this:
32 +
33 +
34 +##precomputed:~/~/https:~/~/data-proxy.ebrains.eu/api/buckets/(% style="background-color:#3498db; color:#ffffff" %)quint-demo(%%)/(% style="background-color:#9b59b6; color:#ffffff" %)tg-ArcSwe_mice_precomputed/hbp-00138_122_381_423_s001.precomputed(%%)##
35 +
36 +this scheme is the same whether you're loading data into the Neuroglancer viewer or specifying an input URL in the export applet.
37 +
38 +=== Viewing 2D Data ===
39 +
18 18  If your dataset is 2D like in the example, you can click the "switch to xy layout" button at the top-right corner of the top-left quadrant of the viewport to use  asingle, 2D viewport:
19 19  
20 20  [[image:image-20220125164416-3.png]]
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92 92  https:~/~/data-proxy.ebrains.eu/your-bucket-name?prefix=your/selected/prefix
93 93  
94 94  [[image:image-20220125191847-3.png]]
95 -
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