{"action":"created","issue":{"url":"https://api.github.com/repos/isetbio/isetbio/issues/190","repository_url":"https://api.github.com/repos/isetbio/isetbio","labels_url":"https://api.github.com/repos/isetbio/isetbio/issues/190/labels{/name}","comments_url":"https://api.github.com/repos/isetbio/isetbio/issues/190/comments","events_url":"https://api.github.com/repos/isetbio/isetbio/issues/190/events","html_url":"https://github.com/isetbio/isetbio/issues/190","id":193208672,"number":190,"title":"Input regime over which the biophysics-based outer-segment IR is valid","user":{"login":"npcottaris","id":3444212,"avatar_url":"https://avatars.githubusercontent.com/u/3444212?v=3","gravatar_id":"","url":"https://api.github.com/users/npcottaris","html_url":"https://github.com/npcottaris","followers_url":"https://api.github.com/users/npcottaris/followers","following_url":"https://api.github.com/users/npcottaris/following{/other_user}","gists_url":"https://api.github.com/users/npcottaris/gists{/gist_id}","starred_url":"https://api.github.com/users/npcottaris/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/npcottaris/subscriptions","organizations_url":"https://api.github.com/users/npcottaris/orgs","repos_url":"https://api.github.com/users/npcottaris/repos","events_url":"https://api.github.com/users/npcottaris/events{/privacy}","received_events_url":"https://api.github.com/users/npcottaris/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-12-02T20:19:20Z","updated_at":"2016-12-04T15:33:05Z","closed_at":null,"body":"**What is the input (isomerization rate / luminance) regime over which the biophysics - based outer segment IR is valid?**\r\n\r\nWe need to establish this for our simulations. To examine this issues I run a simple simulation in which a 100% uniform field stimulus is ramped up and down on a pedestal. The luminance of the pedestal (background) is varied from 100 cd/m2 - 8000 cd/m2.\r\n\r\nResults are shown in the following figure, which plots\r\n- the LMS absorption counts and photocurrent signals in the first two columns (across different luminance levels), \r\n- the modulation in absorption counts and pCurrent as a function of background luminance (log axis) in the top and middle panel of the 3rd column. \r\n\r\n**Observations**:\r\n- The isomerization signal is a linear function of the background level as expected. \r\n- The L/M pCurrent shows a sharp increase for luminances around 1000 cd/m2, and a decline after which approaches zero at around 8000 cd/m2.  We expect some saturation, but do we expect the modulation to go to zero at 8000 cd/m2. This seems kind of early.\r\n- The S pCurrent shows similar dynamics but over a more extended luminance range. This is expected due to the lower S-absorption rate.\r\n\r\n**Questions**:\r\n1. Is the sharp peak between 500-2000 cd/m2 valid, or is it a failure of the model in this regime?\r\n2. Is the decline to zero as we approach 8000 cd/m2 valid, or is it a failure of the model in this regime?\r\n\r\n**Other observations**\r\n3. The pCurrent signals exceed zero pAmps for 1500-4000 cd/m2. Is this another failure of the model in this regime?\r\n4. There are phase shifts between L/M pCurrents above 1000 cd/m2, which is the level at which pCurrents begin to saturate. I suspect that these phase shifts are due to changes in temporal dynamics as we approach saturation and they are different for L and M cones due to their slightly different activation levels by the stimulus.\r\n5. The pCurrent value at the earliest time point is not equal to its value at the latest time point. The initial decline in pCurrent suggest that we need to increase the warm-up period.\r\n\r\n![currentvsluminance](https://cloud.githubusercontent.com/assets/3444212/20848519/73bc90d0-b8a0-11e6-95ba-fdef861ace0a.png)\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/isetbio/isetbio/issues/comments/264710520","html_url":"https://github.com/isetbio/isetbio/issues/190#issuecomment-264710520","issue_url":"https://api.github.com/repos/isetbio/isetbio/issues/190","id":264710520,"user":{"login":"DavidBrainard","id":1158757,"avatar_url":"https://avatars.githubusercontent.com/u/1158757?v=3","gravatar_id":"","url":"https://api.github.com/users/DavidBrainard","html_url":"https://github.com/DavidBrainard","followers_url":"https://api.github.com/users/DavidBrainard/followers","following_url":"https://api.github.com/users/DavidBrainard/following{/other_user}","gists_url":"https://api.github.com/users/DavidBrainard/gists{/gist_id}","starred_url":"https://api.github.com/users/DavidBrainard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DavidBrainard/subscriptions","organizations_url":"https://api.github.com/users/DavidBrainard/orgs","repos_url":"https://api.github.com/users/DavidBrainard/repos","events_url":"https://api.github.com/users/DavidBrainard/events{/privacy}","received_events_url":"https://api.github.com/users/DavidBrainard/received_events","type":"User","site_admin":false},"created_at":"2016-12-04T15:33:05Z","updated_at":"2016-12-04T15:33:05Z","body":"In the first graph, the isomerizations should be a linear function of background for fixed contrast, right?  So the acceleration visible in the plot is just what we'd expect for a linear growth when plotted on a linear vs log scale?  Or am I missing something?  Maybe plot on linear - linear or log - log, and if the latter make it clear visually what a slope of 1 corresponds to.\\\r\n\r\nI think we now understand from Fred the range of backgrounds (500 - 20000 iso/cone-sec) that the model was validated for, and ought to use this as roughly our valid range.\r\n\r\nFrom: Nicolas Cottaris <notifications@github.com>\r\nReply-To: isetbio/isetbio <reply@reply.github.com>\r\nDate: Friday, December 2, 2016 at 4:41 PM\r\nTo: isetbio/isetbio <isetbio@noreply.github.com>\r\nSubject: Re: [isetbio/isetbio] Input regime over which the biophysics-based outer-segment IR is valid (#190)\r\n\r\n\r\nI also ran the simulation with a more transient stimulus (25ms vs. 180ms time constant). Results below.\r\nThe acceleration in modulation around 1000 cd/m2 is almost gone.\r\n\r\n<https://cloud.githubusercontent.com/assets/3444212/20851367/187a7c24-b8ae-11e6-8fd8-8e716e6957af.png>\r\n\r\n—\r\nYou are receiving this because you are subscribed to this thread.\r\nReply to this email directly, view it on GitHub<https://github.com/isetbio/isetbio/issues/190#issuecomment-264570032>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ABGuZUy5x4MNfzvjdQ_EmxpdktUjchFaks5rEJCVgaJpZM4LC80C>.\r\n"}}
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