Changes for page 1. Setting up the working environment
Last modified by puchades on 2025/02/13 10:43
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... ... @@ -29,7 +29,7 @@ 29 29 30 30 === Use the "QUINT image creator" app === 31 31 32 -** ~1. Select images to ingest**32 +**2a. Select images to ingest** 33 33 34 34 Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie. 35 35 ... ... @@ -39,14 +39,16 @@ 39 39 40 40 Click on the "View Brain" button in order to preview your images. 41 41 42 +Now go to the WebAlign app in order to start the registration to atlas. 43 + 42 42 [[image:Screenshot create_brain app.png]] 43 43 44 44 45 -=== Use Image service app === 47 +=== Use Image service app (alt.) === 46 46 47 -** ~1. Start the Image service UI from your webapp**49 +**2b. Start the Image service UI from your webapp** 48 48 49 -** 2.Fill in the requested information:**51 +* ** Fill in the requested information:** 50 50 51 51 - type or paste the URL of the dataset folder containing the images. //Note!// the name of the collab supports only hyphens. 52 52 ... ... @@ -60,24 +60,21 @@ 60 60 61 61 - allow the image service to access your bucket 62 62 63 -[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]] 65 +[[[[image:Skjermbilde 2022-02-08 103443.png||height="199" width="500"]]>>attach:Skjermbilde 2022-02-08 103443.png]] 64 64 65 65 - Store your results: Choose "create a new collab" where your ingested chunks will be stored in the bucket. This option is preferred in order not to overload the Bucket of your current collab. Give a name to your Bucket as well as a name for the collab (bucket slug) (see this illustration for more info) 66 66 67 -[[image:create collab.png ||height="427" width="900"]]69 +[[image:create collab.png]] 68 68 69 69 - Customize your ingestion: 70 70 71 71 - give a name to your ingestion in the "description of ingestion" field. 72 72 73 -**3. For obtaining chunks in DZI format (compatible with WebAlign),** choose "2D" and "not stack of Images". 75 +* ** For obtaining chunks in DZI format (compatible with WebAlign),** choose "2D" and "not stack of Images". 76 +* ** Click //"preview"// in order to preview your task** 77 +* ** Click //"create task"// to launch your ingestion** 78 +* ** Checking results in the Main UI page** 74 74 75 -**4. Click //"preview"// in order to preview your task** 76 - 77 -**5. Click //"create task"// to launch your ingestion** 78 - 79 -**6. Checking results in the Main UI page** 80 - 81 81 Press "Task" in the higher right corner of the window. 82 82 83 83 When creating the task, a red banner is displayed in the "Create Task" view if something goes wrong for instance. ... ... @@ -100,13 +100,13 @@ 100 100 101 101 === Opening a sample dataset === 102 102 103 -Demo dataset is loaded using the file: **demo_mouse_data_start** 102 +Demo dataset is loaded using the file: **demo_mouse_data_start.waln** 104 104 105 -You can see the result of a finished anchoring by choosing the file: **demo_mouse_data** 104 +You can see the result of a finished anchoring by choosing the file: **demo_mouse_data.waln** 106 106 107 107 === Opening a private dataset === 108 108 109 -After you have uploaded your images to the bucket and ingested your images with the Image service, this has generated DZI chunks. These DZI files are used by WebAlign.108 +After you have uploaded your images to the bucket and ingested your images with the QUINT Image creator app, this has generated DZIP chunks. These DZIP files are used by WebAlign. 110 110 111 111 ~1. Start a new registration by pressing "create new series", the UI will ask you for the name of the collab where DZI chunks are stored. E.g. my-collab-name 112 112