{"action":"created","comment":{"url":"https://api.github.com/repos/ome/training-notebooks/pulls/comments/235357152","pull_request_review_id":177201273,"id":235357152,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIzNTM1NzE1Mg==","diff_hunk":"@@ -0,0 +1,702 @@\n+{\n+ \"cells\": [\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"# Image Segmentation using the idr0021 dataset\\n\",\n+    \"\\n\",\n+    \"This notebook uses the idr0021 dataset (original: [idr0021-lawo-pericentriolarmaterial/experimentA](http://idr.openmicroscopy.org/webclient/?show=project-51)) and tries to reproduce some of the analysis published in ['Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material'](https://doi.org/10.1038/ncb2591). In particular we're trying to get a figure similar to [Figure 1](https://www.nature.com/articles/ncb2591/figures/1) of the article. \\n\",\n+    \"\\n\",\n+    \"Each user has a partial copy of the dataset ('Lab1' / YOUR USER / Project: 'idr0021'). Some of the images are also part of the dataset 'R-dataset' which you can use for practicing the segmentation and annotation steps.\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"**Exercise:** Go to https://outreach.openmicroscopy.org , log in as your given user, and find the dataset ('Lab1' / YOUR USER / Project: 'R-dataset'). Leave the window open, as you will use OMERO.web to check the results as we're going along.\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"## How to use this notebook\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"The grey blocks with the In\\\\[ \\\\] notation to the left are code blocks. Click on a block to select it and click the play button in the toolbar to execute the block of code (alternatively hold SHIFT key and hit RETURN). The notation will change to In\\\\[*\\\\] to indicate that this code is currently running. The output is displayed below the block. Wait for it to finish. When the execution is finished it will change to ln\\\\[1\\\\] showing that this was the first block of code you ran (ln\\\\[2\\\\], ln\\\\[3\\\\], ... for the next executed code blocks). \\n\",\n+    \"\\n\",\n+    \"As we go through the notebook you're expected to run the code blocks in order (unless explicitely mentioned otherwise).\\n\",\n+    \"\\n\",\n+    \"Here's an example:\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"message(\\\"Just wait for a bit...\\\")\\n\",\n+    \"Sys.sleep(3)\\n\",\n+    \"message(\\\"Done.\\\")\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"You can change the code and run the block again.\\n\",\n+    \"\\n\",\n+    \"**Exercise:** Change the message which is printed and run it again.\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"## Let's get started...\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"Load the necessary [romero-gateway](https://github.com/ome/rOMERO-gateway) and [EBImage](https://bioconductor.org/packages/release/bioc/html/EBImage.html) library. We're currently using romero-gateway 0.4.3, EBImage 4.13.0 with R 3.4.1 . \"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"library(romero.gateway)\\n\",\n+    \"library(EBImage, warn.conflicts = FALSE)\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"## Log into the OMERO server\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"code\",\n+   \"execution_count\": null,\n+   \"metadata\": {},\n+   \"outputs\": [],\n+   \"source\": [\n+    \"user_name = readline('Username: ')\\n\",\n+    \"user_password <- getPass::getPass('OMERO password: ')\\n\",\n+    \"server <- OMEROServer(host = 'outreach.openmicroscopy.org', username=user_name, password=user_password, port= as.integer(4064))\\n\",\n+    \"server <- connect(server)\\n\",\n+    \"paste('Successfully logged in as', server@user$getUserName())\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"## Load and display an image\"\n+   ]\n+  },\n+  {\n+   \"cell_type\": \"markdown\",\n+   \"metadata\": {},\n+   \"source\": [\n+    \"Load an image from the example dataset 'R-dataset' (these images are part of the original 'CDK5RAP2-C' dataset).\\n\",\n+    \"\\n\",\n+    \"**Exercise:** Go to the image 'siControl_N20_Cep215_I_20110411_Mon-1509_0_SIR_PRJ.dv' in your 'R-dataset', find the 'Image ID' and copy/paste it below. You can use a different image of the dataset if you like, but I recommend that one because it nicely shows the toroid centrioles.\"","path":"R/idr0021 - Segmentation.ipynb","position":116,"original_position":116,"commit_id":"8adf8a95881932a8dcd69e15705ea14aafaeaf04","original_commit_id":"8adf8a95881932a8dcd69e15705ea14aafaeaf04","user":{"login":"pwalczysko","id":2478303,"node_id":"MDQ6VXNlcjI0NzgzMDM=","avatar_url":"https://avatars1.githubusercontent.com/u/2478303?v=4","gravatar_id":"","url":"https://api.github.com/users/pwalczysko","html_url":"https://github.com/pwalczysko","followers_url":"https://api.github.com/users/pwalczysko/followers","following_url":"https://api.github.com/users/pwalczysko/following{/other_user}","gists_url":"https://api.github.com/users/pwalczysko/gists{/gist_id}","starred_url":"https://api.github.com/users/pwalczysko/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pwalczysko/subscriptions","organizations_url":"https://api.github.com/users/pwalczysko/orgs","repos_url":"https://api.github.com/users/pwalczysko/repos","events_url":"https://api.github.com/users/pwalczysko/events{/privacy}","received_events_url":"https://api.github.com/users/pwalczysko/received_events","type":"User","site_admin":false},"body":"Leave out the sentence aoubt ``You can use a different image if you like....`` It is too long. Nobody knows what the centrioles are at this stage. I guess they will understand that they can use another image. \r\n\r\nPossibly\r\n\r\n\r\n``Exercise: Find in OMERO.web an ImageID of a different image and display it in R.``","created_at":"2018-11-21T11:52:08Z","updated_at":"2018-11-21T11:52:08Z","html_url":"https://github.com/ome/training-notebooks/pull/28#discussion_r235357152","pull_request_url":"https://api.github.com/repos/ome/training-notebooks/pulls/28","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/ome/training-notebooks/pulls/comments/235357152"},"html":{"href":"https://github.com/ome/training-notebooks/pull/28#discussion_r235357152"},"pull_request":{"href":"https://api.github.com/repos/ome/training-notebooks/pulls/28"}},"in_reply_to_id":235353189},"pull_request":{"url":"https://api.github.com/repos/ome/training-notebooks/pulls/28","id":231269473,"node_id":"MDExOlB1bGxSZXF1ZXN0MjMxMjY5NDcz","html_url":"https://github.com/ome/training-notebooks/pull/28","diff_url":"https://github.com/ome/training-notebooks/pull/28.diff","patch_url":"https://github.com/ome/training-notebooks/pull/28.patch","issue_url":"https://api.github.com/repos/ome/training-notebooks/issues/28","number":28,"state":"open","locked":false,"title":"Add first version of the idr0021 segmentation notebook","user":{"login":"dominikl","id":6575139,"node_id":"MDQ6VXNlcjY1NzUxMzk=","avatar_url":"https://avatars2.githubusercontent.com/u/6575139?v=4","gravatar_id":"","url":"https://api.github.com/users/dominikl","html_url":"https://github.com/dominikl","followers_url":"https://api.github.com/users/dominikl/followers","following_url":"https://api.github.com/users/dominikl/following{/other_user}","gists_url":"https://api.github.com/users/dominikl/gists{/gist_id}","starred_url":"https://api.github.com/users/dominikl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dominikl/subscriptions","organizations_url":"https://api.github.com/users/dominikl/orgs","repos_url":"https://api.github.com/users/dominikl/repos","events_url":"https://api.github.com/users/dominikl/events{/privacy}","received_events_url":"https://api.github.com/users/dominikl/received_events","type":"User","site_admin":false},"body":"Adds a notebook which performs the  idr0021 segmentation completely in R (to be used for the Cambridge workshop 6th Dec).\r\n\r\nTest on : https://ome-lochy.openmicroscopy.org/jupyterhub-internal  (training-notebooks:master_merge_daily)","created_at":"2018-11-15T17:06:58Z","updated_at":"2018-11-21T11:52:08Z","closed_at":null,"merged_at":null,"merge_commit_sha":"bf8993e82703309b44efe1798fe06a058fa38f5c","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/ome/training-notebooks/pulls/28/commits","review_comments_url":"https://api.github.com/repos/ome/training-notebooks/pulls/28/comments","review_comment_url":"https://api.github.com/repos/ome/training-notebooks/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ome/training-notebooks/issues/28/comments","statuses_url":"https://api.github.com/repos/ome/training-notebooks/statuses/8adf8a95881932a8dcd69e15705ea14aafaeaf04","head":{"label":"dominikl:master","ref":"master","sha":"8adf8a95881932a8dcd69e15705ea14aafaeaf04","user":{"login":"dominikl","id":6575139,"node_id":"MDQ6VXNlcjY1NzUxMzk=","avatar_url":"https://avatars2.githubusercontent.com/u/6575139?v=4","gravatar_id":"","url":"https://api.github.com/users/dominikl","html_url":"https://github.com/dominikl","followers_url":"https://api.github.com/users/dominikl/followers","following_url":"https://api.github.com/users/dominikl/following{/other_user}","gists_url":"https://api.github.com/users/dominikl/gists{/gist_id}","starred_url":"https://api.github.com/users/dominikl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dominikl/subscriptions","organizations_url":"https://api.github.com/users/dominikl/orgs","repos_url":"https://api.github.com/users/dominikl/repos","events_url":"https://api.github.com/users/dominikl/events{/privacy}","received_events_url":"https://api.github.com/users/dominikl/received_events","type":"User","site_admin":false},"repo":{"id":133776424,"node_id":"MDEwOlJlcG9zaXRvcnkxMzM3NzY0MjQ=","name":"training-notebooks","full_name":"dominikl/training-notebooks","private":false,"owner":{"login":"dominikl","id":6575139,"node_id":"MDQ6VXNlcjY1NzUxMzk=","avatar_url":"https://avatars2.githubusercontent.com/u/6575139?v=4","gravatar_id":"","url":"https://api.github.com/users/dominikl","html_url":"https://github.com/dominikl","followers_url":"https://api.github.com/users/dominikl/followers","following_url":"https://api.github.com/users/dominikl/following{/other_user}","gists_url":"https://api.github.com/users/dominikl/gists{/gist_id}","starred_url":"https://api.github.com/users/dominikl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dominikl/subscriptions","organizations_url":"https://api.github.com/users/dominikl/orgs","repos_url":"https://api.github.com/users/dominikl/repos","events_url":"https://api.github.com/users/dominikl/events{/privacy}","received_events_url":"https://api.github.com/users/dominikl/received_events","type":"User","site_admin":false},"html_url":"https://github.com/dominikl/training-notebooks","description":" 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