Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -1,4 +1,4 @@
1		-== To set up the working environment: ==
	1	+== To set up your working environment: ==
2	2
3	3	1. [[Register>>url:https://ebrains.eu/register/]] for an EBRAINS account, login, and set up a [[private collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/]].
4	4	1. Initialise the Bucket by clicking on Bucket in the navigation panel -> Create Bucket.
...	...	@@ -13,12 +13,44 @@
13	13	1. Repeat this for all the relevant Community Apps.
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 use Image service UI? ==
	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.tif
	23	+
	24	+**2. Image ingestion**
	25	+
	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	+
	28	+(% class="wikigeneratedid" %)
	29	+=== ===
	30	+
	31	+=== Use the "QUINT image creator" app ===
	32	+
	33	+**~1. Select images to ingest**
	34	+
	35	+Shift-Click on your images in order to select them and press the "create brain from selection" button. Choose a name for your serie.
	36	+
	37	+The App will automatically generate the files for you. Monitor the progress under the "processing" tab and on the two dashboards on the left.
	38	+
	39	+When the ingestion is finished, your serie will appear under the "Prepared Brains" tab.
	40	+
	41	+Click on the "View Brain" button in order to preview your images.
	42	+
	43	+
	44	+
	45	+
	46	+== ==
	47	+
	48	+=== Use Image service app ===
	49	+
	50	+**~1. Prepare your images before upload by naming them according this naming convention:**
	51	+
	52	+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).
	53	+
22	22	Example: tg2345_MMSH_s001_segmentation.png
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"//)
...	...	@@ -29,13 +29,13 @@
29	29
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		-E.g. https:~/~/data-proxy.ebrains.eu/api/buckets/name-of-my-collab
	64	+E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab
33	33
34		- - you can filter the data using RegEx expressions. E.g. name_of_the_data_folder\/.*\.jpg$ (for filtering jpeg files only).
	66	+ - you can filter the data using RegEx expressions. E.g. name_of_the_data_file.*\.jpg$ (for filtering jpeg files only). Or e.g hbp-00173_262_1366_1827.*\.tif$ for tiff files.
35	35
36	36	- If your URL is valid, you will see the list of files by pressing "yes". Paste the name of the file you want to select. You can go back to the previous step  by pressing "back"
37	37
38		- - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/buckets/name-of-my-collab?prefix=name_of_the_data_folder
	70	+ - Or use a prefix: E.g. https:~/~/data-proxy.ebrains.eu/api/v1/buckets/name-of-my-collab?prefix=name_of_the_data_folder
39	39
40	40	- allow the image service to access your bucket
41	41
...	...	@@ -73,6 +73,8 @@
73	73
74	74	WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.  Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system. The output of WebAlign can be used for analysis in the online QUINT workflow.
75	75
	108	+Online user manual: [[https:~~/~~/webalign.readthedocs.io/en/latest/>>https://webalign.readthedocs.io/en/latest/]]
	109	+
76	76	The view can be magnified using the 4-arrow "X" symbol in the top-right corner.
77	77
78	78	=== Opening a sample dataset ===