Changes for page 1. Setting up the working environment
Last modified by puchades on 2025/02/13 10:43
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... ... @@ -10,23 +10,46 @@ 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 -== How to useImageserviceUI? ==16 +== How to prepare your images? == 17 17 18 18 **~1. Prepare your images before upload by naming them according this naming convention:** 19 19 20 20 The ID should be unique to the particular brain section and in the format sXXX, with XXX representing the section number. The section number should reflect the serial order and spacing of the sections (e.g., s002, s006, s010 for every 4^^th^^ section starting with section 2). 21 21 22 -Example: tg2345_MMSH_s001 _segmentation.png22 +Example: tg2345_MMSH_s001.tif 23 23 24 24 - Upload the images you want to work with into the bucket of your collab using the Data proxy (press on //"Bucket"//) 25 25 26 -**2. Start theImageserviceUI from your webapp**26 +**2. Image ingestion** 27 27 28 - **3.Fill in the requestedinformation:**28 +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: 29 29 30 +=== Use the "QUINT image creator" app === 31 + 32 +**~1. Select images to ingest** 33 + 34 +Shift-Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie. 35 + 36 +The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left. 37 + 38 +When the ingestion is finished, your serie will appear under the "Prepared Brains" tab. 39 + 40 +Click on the "View Brain" button in order to preview your images. 41 + 42 + 43 + 44 + 45 +== == 46 + 47 +=== Use Image service app === 48 + 49 +**~1. Start the Image service UI from your webapp** 50 + 51 +**2. Fill in the requested information:** 52 + 30 30 - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens. 31 31 32 32 E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab