{"__v":2,"_id":"56de30df9ca83e17000cbc59","category":{"__v":19,"_id":"54f7a7be0a3cbb0d00d666fb","pages":["54f7a95354182d2100c9d057","54f7ad293607243500de2496","54f7ae7d0a3cbb0d00d66705","54f7b0013607243500de249b","54f7b4360a3cbb0d00d6670c","54f7c71154182d2100c9d073","54fa5205961fea21009206a9","54fa55e1c6db4517005b0147","54fddf642804410d00ee8a2a","5509fd2bdfed731900b81863","552dfa862594f70d001b2c48","552dfab3a702770d00d96d5b","552dfaca2594f70d001b2c4a","55d68d2c250d7d0d00427478","55d68d3bae529e0d00d34edb","5611dd433ca69417008981af","5679bca976cd370d003c1183","56de30df9ca83e17000cbc59","56eadf62199f7317006eb4db"],"project":"5476bf0f817e8d080031f988","version":"5476bf10817e8d080031f98b","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-03-05T00:47:58.582Z","from_sync":false,"order":4,"slug":"instructions","title":"Capabilities"},"parentDoc":null,"project":"5476bf0f817e8d080031f988","user":"55e4edf4177b6e0d00333165","version":{"__v":17,"_id":"5476bf10817e8d080031f98b","project":"5476bf0f817e8d080031f988","createdAt":"2014-11-27T06:05:04.263Z","releaseDate":"2014-11-27T06:05:04.263Z","categories":["5476bf10817e8d080031f98c","5477c46cf3736008009e9eb5","5477c474f3736008009e9eb6","5477c47ef3736008009e9eb7","5477c48ff3736008009e9eb8","5477c4948deb230800808bf0","54e68328154f8e0d0007b55c","54e90194c8e0c00d007ac061","54eed2275bf74a0d00ef4076","54f7a7be0a3cbb0d00d666fb","559b0ebf7ae7f80d0096d871","55d697f9ae529e0d00d34f03","562d4dcc8c6e5a0d00d6ed1d","562e591c4376430d006f17e0","568f0e73bdb9260d00149d8c","5719542aac1e2e0e001834c6","57a14a8ed778850e0047e230"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-03-08T01:54:39.025Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":true,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":21,"body":"[block:callout]\n{\n  \"type\": \"danger\",\n  \"body\": \"This feature is still technically under development and this page may change.\"\n}\n[/block]\nThere are two steps in bacterial transformation: plating cells and picking colonies.  Each of these steps has an associated instruction.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Instructions and Parameters\"\n}\n[/block]\nBacterial spreading is done using a modified Tecan Omni liquid handler. The specified volume of bacteria is aspirated from the `from` well and spread evenly on the agar-containing `to` well.  Bacteria can be spread on either a 1-well SBS format agar-containing rectangular plate or a 6-well SBS format plate containing agar. \nSpreading streaks the bacteria on the plate in a fixed number of linear motions. 5 streaks for 6-well plates and 10 streak for 1-well plates. The pattern is illustrated in this image:\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/jmcLOhalTiWewF4RAN3H_streak.png\",\n        \"streak.png\",\n        \"520\",\n        \"248\",\n        \"#315c82\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\nReasonable volumes for spreading resulting in single colonies are 25-100uL per well in 6-well plates and 500-1000uL for 1-well plates.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"op\\\": \\\"spread\\\",\\n  \\\"from\\\": well,\\n  \\\"to\\\": well,\\n  \\\"volume\\\": volume\\n}\",\n      \"language\": \"json\",\n      \"name\": \"spread\"\n    }\n  ]\n}\n[/block]\nOnce bacteria have grown, you can instruct a modified Tecan Omni to pick colonies from the agar-containing `from` well(s) into the `to` well(s) you specify. The modified Tecan Omni takes pictures of the source plate and uses computer vision to detect and rank colonies on the plate. Data produced by the analysis of the source container is returned with the `dataref`.\n\nSpecifying a list of `from` wells allows the analysis algorithm to choose the best colonies amongst those wells to be picked into the `to` wells.\n\nThe `autopick` instruction takes groups of `from` and `to` dictionaries provided that all the `from` wells in all of the groups come from the same container. This allows the analysis algorithm to recognize colonies from all wells at once shortening the analysis time and saving results to a single `dataref`.\n\nEach group also contains an optional `min_abort`. If the number of colonies found is less than `min_abort`, the remainder of the run will be aborted. Setting `min_abort` to 0 allows the run to continue no matter how many colonies were identified.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"op\\\": \\\"autopick\\\",\\n  \\\"dataref\\\": string,\\n  \\\"criteria\\\": {},\\n  \\\"groups\\\": [\\n    {\\n      \\\"from\\\": [\\n        well\\n      ],\\n      \\\"to\\\": [\\n        well\\n      ],\\n      \\\"min_abort\\\": int\\n    }\\n  ]\\n}\",\n      \"language\": \"json\",\n      \"name\": \"autopick\"\n    }\n  ]\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Device\"\n}\n[/block]\nSpreading of bacteria onto a single-well rectangular dish is done by Tecan ADP modules on a Omni robotic system. Colony picking is done using proprietary Transcriptic computer vision systems linked to Tecan ADP modules.","excerpt":"","slug":"spreading-bacteria-colony-picking","type":"basic","title":"Spreading Bacteria & Colony Picking"}

Spreading Bacteria & Colony Picking


[block:callout] { "type": "danger", "body": "This feature is still technically under development and this page may change." } [/block] There are two steps in bacterial transformation: plating cells and picking colonies. Each of these steps has an associated instruction. [block:api-header] { "type": "basic", "title": "Instructions and Parameters" } [/block] Bacterial spreading is done using a modified Tecan Omni liquid handler. The specified volume of bacteria is aspirated from the `from` well and spread evenly on the agar-containing `to` well. Bacteria can be spread on either a 1-well SBS format agar-containing rectangular plate or a 6-well SBS format plate containing agar. Spreading streaks the bacteria on the plate in a fixed number of linear motions. 5 streaks for 6-well plates and 10 streak for 1-well plates. The pattern is illustrated in this image: [block:image] { "images": [ { "image": [ "https://files.readme.io/jmcLOhalTiWewF4RAN3H_streak.png", "streak.png", "520", "248", "#315c82", "" ] } ] } [/block] Reasonable volumes for spreading resulting in single colonies are 25-100uL per well in 6-well plates and 500-1000uL for 1-well plates. [block:code] { "codes": [ { "code": "{\n \"op\": \"spread\",\n \"from\": well,\n \"to\": well,\n \"volume\": volume\n}", "language": "json", "name": "spread" } ] } [/block] Once bacteria have grown, you can instruct a modified Tecan Omni to pick colonies from the agar-containing `from` well(s) into the `to` well(s) you specify. The modified Tecan Omni takes pictures of the source plate and uses computer vision to detect and rank colonies on the plate. Data produced by the analysis of the source container is returned with the `dataref`. Specifying a list of `from` wells allows the analysis algorithm to choose the best colonies amongst those wells to be picked into the `to` wells. The `autopick` instruction takes groups of `from` and `to` dictionaries provided that all the `from` wells in all of the groups come from the same container. This allows the analysis algorithm to recognize colonies from all wells at once shortening the analysis time and saving results to a single `dataref`. Each group also contains an optional `min_abort`. If the number of colonies found is less than `min_abort`, the remainder of the run will be aborted. Setting `min_abort` to 0 allows the run to continue no matter how many colonies were identified. [block:code] { "codes": [ { "code": "{\n \"op\": \"autopick\",\n \"dataref\": string,\n \"criteria\": {},\n \"groups\": [\n {\n \"from\": [\n well\n ],\n \"to\": [\n well\n ],\n \"min_abort\": int\n }\n ]\n}", "language": "json", "name": "autopick" } ] } [/block] [block:api-header] { "type": "basic", "title": "Device" } [/block] Spreading of bacteria onto a single-well rectangular dish is done by Tecan ADP modules on a Omni robotic system. Colony picking is done using proprietary Transcriptic computer vision systems linked to Tecan ADP modules.