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Author

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1		-XWiki.tomazvieira
	1	+XWiki.puchades

Content

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1		-== What is webilastik? ==
	1	+== What is Webilastik? ==
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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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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.
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8		-== How to use webilastik ==
	8	+== How to use Webilastik ==
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10	10	=== Opening a sample Dataset ===
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19	19	=== Opening a Dataset from the data-proxy ===
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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		-\\##precomputed:~/~/https:~/~/data-proxy.ebrains.eu/api/buckets/(% style="color: rgb(255, 255, 255); background-color: rgb(52, 152, 219)" %)my-bucket-name(% style="color: rgb(255, 255, 255); background-color: rgb(155, 89, 182)" %)/path/inside/your/bucket(%%)##
	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(%%)##
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24		-So, for example, to load the sample data inside the (% style="color: rgb(255, 255, 255); background-color: rgb(52, 152, 219)" %)quint-demo(%%) bucket, under the path (% style="color: rgb(255, 255, 255); background-color: rgb(155, 89, 182)" %)tg-ArcSwe_mice_precomputed/hbp-00138_122_381_423_s001.precomputed(% style="color:#000000" %) (%%) like in the example below:
	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:
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27	27	[[image:image-20220128142757-1.png]]
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29		-=== ===
	29	+=== ===
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31	31	you would type a URL like this:
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34		-##precomputed:~/~/https:~/~/data-proxy.ebrains.eu/api/buckets/(% style="color: rgb(255, 255, 255); background-color: rgb(52, 152, 219)" %)quint-demo(%%)/(% style="color: rgb(255, 255, 255); background-color: rgb(155, 89, 182)" %)tg-ArcSwe_mice_precomputed/hbp-00138_122_381_423_s001.precomputed(%%)##
	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(%%)##
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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.
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