Last modified by puchades on 2022/09/30 16:01
From version 33.1
edited by tomazvieira
on 2022/02/22 16:02
Change comment: There is no comment for this version
To version 43.1
edited by tomazvieira
on 2022/09/11 15:17
Change comment: Uploaded new attachment "webilastik_bucket_paths.png", version {1}

Summary

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7 7  
8 8  == How to use Webilastik ==
9 9  
10 -=== Opening a sample Dataset ===
10 +(% class="wikigeneratedid" %)
11 +Webilastik is a web application that can be accessed on [[https:~~/~~/app.ilastik.org>>https://app.ilastik.org]]. We suggest using it via the Chrome (or Chromium) web browser for now, since most of the testing has been done in this browser and subtle differences between browsers might cause unexpected behavior in the application.
11 11  
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 +(% class="wikigeneratedid" %)
14 +You can find the webilastik application at [[https:~~/~~/app.ilastik.org/>>url:https://app.ilastik.org/]]. You can also go directly to the [[application page>>https://app.ilastik.org/public/nehuba/index.html#!%7B%22layout%22:%22xy%22%7D]].
13 13  
16 +Webilastik is an overlay on top of other data viewers. In particular, this implementation uses [[Neuroglancer>>https://github.com/google/neuroglancer]] as an underlying data viewer, so if you're familiar with its controls you can still use them when using webilastik.
17 +
18 +=== Moving the controls window ===
19 +
20 +You can move the webilastik controls around the screen by clicking and dragging on the header:
21 +
22 +[[image:webilastik_click_and_drag.png]]
23 +
24 +
25 +=== Opening a Dataset ===
26 +
27 +Like in vanilla Neuroglancer, you add datasets to the viewer by clicking the "+" button at the top of the viewer:
28 +
29 +[[image:webilastik_click_plus_sign_in_neuroglancer.png||height="200"]]
30 +
31 +
32 +You should be presented with a popup prompt where you can type in the URL of a dataset you want to view, in the format typically used by Neuroglancer. There are a few sample datasets hosted in webilastik:
33 +
34 +precomputed:~/~/https:~/~/app.ilastik.org/public/images/mouse1.precomputed
35 +
36 +precomputed:~/~/https:~/~/app.ilastik.org/public/images/mouse2.precomputed
37 +
38 +precomputed:~/~/https:~/~/app.ilastik.org/public/images/mouse3.precomputed
39 +
14 14  precomputed:~/~/https:~/~/app.ilastik.org/public/images/c_cells_2.precomputed
15 15  
42 +precomputed:~/~/https:~/~/app.ilastik.org/public/images/c_cells_3.precomputed
43 +
44 +
45 +After you type or paste the URL into the "Source" field, neuroglancer should recognize the shape and number of channels in the image. You can the click "Add Layer" to open the dataset in the viewer.
46 +
16 16  [[image:image-20220125164204-2.png]]
17 17  
18 18  
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21 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 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 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:
55 +So, for example, to load the sample data inside the (% style="background-color:#3498db; color:#ffffff" %)ana-workshop(%%) 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 25  
26 26  
27 27  [[image:image-20220128142757-1.png]]
28 28  
29 -=== ===
60 +=== ===
30 30  
31 31  you would type a URL like this:
32 32  
33 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(%%)##
65 +##precomputed:~/~/https:~/~/data-proxy.ebrains.eu/api/buckets/(% style="background-color:#3498db; color:#ffffff" %)ana-workshop(%%)/(% style="background-color:#9b59b6; color:#ffffff" %)tg-ArcSwe_mice_precomputed/hbp-00138_122_381_423_s001.precomputed(%%)##
35 35  
36 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 37  
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45 45  
46 46  [[image:image-20220125164557-4.png]]
47 47  
79 +You can also click the
80 +
81 +==== A Note on Neuroglancer and 2D data ====
82 +
83 +
84 +Neuroglancer interprets all data as 3D, and visualizing a 2D image is interpreted as a single flat slice of data in 3D space. Scrolling in Neuroglancer can make the viewer go past this single slice of data, effectively hiding it from view. You can see the current viewer position in the top-left corner of the viewport, and you can edit those coordinates to reset the viewer to a position where your data is present and therefore visible (usually z=0 for 2D data):
85 +
86 +
87 +[[image:image-20220222161022-1.png]]
88 +
89 +(% class="wikigeneratedid" %)
90 +Alternatively, once you have a compute session running you can also click the "Reset" button in the lower-right corner of the viewer to move the viewer back to the center of your datasets:
91 +
92 +(% class="wikigeneratedid" %)
93 +[[image:webilastik_click_recenter_button.png]]
94 +
95 +== Allocating a Compute Session ==
96 +
97 +Normal ilastik operation can be computationally intensive, requiring dedicated compute resources to be allocated to every user working with it.
98 +
99 +
100 +The "Session Management" widget allows you to request a compute session where webilastik will run; Select a session duration and click 'Create' to create a new compute session. Eventually the compute session will be allocated, opening up the other workflow widgets.
101 +
102 +
103 +
48 48  == Training the Pixel Classifier ==
49 49  
50 50  === Selecting Image Features ===
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