Last modified by puchades on 2022/09/30 16:01
From version 30.1
edited by tomazvieira
on 2022/02/22 15:31
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To version 41.1
edited by tomazvieira
on 2022/09/11 12:43
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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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37 37  
38 38  === Viewing 2D Data ===
39 39  
40 -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:
71 +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 a single, 2D viewport:
41 41  
42 42  [[image:image-20220125164416-3.png]]
43 43  
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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 +(% class="wikigeneratedid" %)
96 +== Allocating a Compute Session ==
97 +
98 +Normal ilastik operation can be computationally intensive, requiring dedicated compute resources to be allocated to every user working with it.
99 +
100 +
101 +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.
102 +
103 +
104 +
48 48  == Training the Pixel Classifier ==
49 49  
50 50  === Selecting Image Features ===
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73 73  
74 74  You must have the "training" tab as the frontmost visible tab in order to start adding brush strokes (in neuroglancer you can click the name of the raw data tab to hide it, for example):
75 75  
76 -[[image:image-20220125170609-3.png]]
133 +[[image:image-20220222151117-1.png]]
77 77  
135 +
78 78  The status display in this applet will show "training on [datasource url]" when you're in training mode.
79 79  
80 80  Now you can start adding brush strokes. Select a color from the color picker, check the "Enable Brushing" checkbox to enable brushing (and disable navigation), and click and drag over the image to add brush strokes. Ilastik will map each used color to a "class", and will try to figure out a class for every pixel in the image based on the examples provided by the brush strokes. By painting, you provide ilastik with samples of what a pixel in that particular class should look like. The following image shows an example with 2 classes: teal, representing the "foreground" or the "cell class", and magenta, representing the "background" class.
81 81  
82 -[[image:image-20220125171324-4.png]]
140 +[[image:image-20220222153157-4.png]]
83 83  
84 -Once you have some image features selected and at least one brush annotation, ilastik will automatically use your examples to predict what classes the rest of your dataset should be, displaying the results in a "predictions" tab.
142 +Once you have some image features selected and some brush annotation of at least 2 colors, you can check "Live Update" and ilastik will automatically use your examples to predict what classes the rest of your dataset should be, displaying the results in a "predictions" tab.
85 85  
86 -[[image:image-20220125171715-5.png]]
144 +[[image:image-20220222153610-5.png]]
87 87  
146 +
147 +You can keep adding or removing brush strokes to improve your predictions.
148 +
88 88  You can adjust the display settings of the overlay predictions layer as you would in vanilla neuroglancer:
89 89  
90 90  1. right-click the predictions Neuroglancer tab to reveal the "rendering" options
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