Changes for page 1. Setting up the working environment
Last modified by puchades on 2025/02/13 10:43
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... ... @@ -10,7 +10,7 @@ 10 10 1. To install Collaboratory Apps, click on the + Create button (top right corner). 11 11 1. Give the page a Title (for example, WebAlign), select the Community App option, and click Create. 12 12 1. Select the App to install (for example, WebAlign), and click Save and View. 13 -1. Repeat this for all the relevant Community Apps. 13 +1. Repeat this for all the relevant Community Apps. You will need, "QUINT Image creator app"; "WebAlign"; "WebWarp"; "LocaliZoom" and "MeshView". 14 14 1. Navigate between the Apps in the navigation panel. File transfer between the Apps is through the Bucket. 15 15 16 16 == How to prepare your images? == ... ... @@ -21,13 +21,12 @@ 21 21 22 22 Example: tg2345_MMSH_s001.tif 23 23 24 +- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//) 25 + 24 24 **2. Image ingestion** 25 25 26 26 Two alternatives are available, the QUINT image creator app, which is automatically creating the necessary files for downstream analyses in your collab. Or, you can use the image service app which is able to create image tiles in different formats. The steps for preparing your files are described bellow: 27 27 28 -(% class="wikigeneratedid" %) 29 -=== === 30 - 31 31 === Use the "QUINT image creator" app === 32 32 33 33 **~1. Select images to ingest** ... ... @@ -41,24 +41,16 @@ 41 41 Click on the "View Brain" button in order to preview your images. 42 42 43 43 43 + 44 44 45 - 46 46 == == 47 47 48 48 === Use Image service app === 49 49 50 -**~1. Prepareyour imagesbeforeuploadby namingthem accordingthis naming convention:**49 +**~1. Start the Image service UI from your webapp** 51 51 52 - TheID should be unique to the particularbrainsection and in theformat sXXX, with XXX representing the section number. Thesection number shouldreflect the serial order and spacing ofthe sections (e.g., s002, s006, s010 forevery 4^^th^^ section starting with section2).51 +**2. Fill in the requested information:** 53 53 54 -Example: tg2345_MMSH_s001_segmentation.png 55 - 56 -- Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//) 57 - 58 -**2. Start the Image service UI from your webapp** 59 - 60 -**3. Fill in the requested information:** 61 - 62 62 - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens. 63 63 64 64 E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab