| 474c639 | Stephanie Johnson | 22 May 2014, 22:12:35 UTC | Debugging previous two commits | 22 May 2014, 22:12:35 UTC |
| dd5fb7f | Stephanie Johnson | 22 May 2014, 19:06:00 UTC | Modified UserSpotSelection to save both raw and smoothed intensities and FRET values | 22 May 2014, 19:06:00 UTC |
| 06c138c | Stephanie Johnson | 22 May 2014, 19:00:34 UTC | Plot lines at 0 on intensity plots and 0 and 1 on FRET plots for UserSpotSelection | 22 May 2014, 19:00:34 UTC |
| dcd86a2 | Stephanie Johnson | 22 May 2014, 16:45:07 UTC | Added the option to see an average over 10 frames anywhere in teh movie in UserSpotSelection | 22 May 2014, 16:45:07 UTC |
| 345f88a | Stephanie Johnson | 22 May 2014, 16:24:00 UTC | Fixed a bug if movie is less than 100 frames | 22 May 2014, 16:24:00 UTC |
| de20188 | Stephanie Johnson | 21 May 2014, 01:56:49 UTC | Fixed some bugs involving ExtractROI | 21 May 2014, 01:56:49 UTC |
| 1d63fe1 | Stephanie Johnson | 19 May 2014, 04:26:08 UTC | Mostly debugged the new GaussFit routine although the last part of CalcIntensitiesV2 was taking forever | 19 May 2014, 04:26:08 UTC |
| 20bb2ee | Stephanie Johnson | 19 May 2014, 02:37:42 UTC | Debugged FindSpotVars | 19 May 2014, 02:37:42 UTC |
| 7ba10f5 | Stephanie Johnson | 19 May 2014, 01:19:25 UTC | Also got UserSpotSelection to use the new localcen functionality of ExtractROI | 19 May 2014, 01:19:25 UTC |
| ab1ac64 | Stephanie Johnson | 19 May 2014, 01:16:19 UTC | Fixed a bug in ExtractROIs return localcen functionality, and made PlayMovie use this new functionality instead of its own separate subfunction | 19 May 2014, 01:16:19 UTC |
| 9bbd8ec | Stephanie Johnson | 15 May 2014, 23:44:33 UTC | Implemented EndInjectFrame | 15 May 2014, 23:44:33 UTC |
| 28ea1c5 | Stephanie Johnson | 15 May 2014, 01:51:00 UTC | Implemented final part of the new Gauss fit routine, where background is subtracted frame by frame | 15 May 2014, 01:51:00 UTC |
| 9405a80 | Stephanie Johnson | 14 May 2014, 20:05:18 UTC | Integrated the new Fit2DGaussToSpot into smFRET to find the variances for each spot | 14 May 2014, 20:05:18 UTC |
| 75d1f63 | Stephanie Johnson | 13 May 2014, 22:54:17 UTC | Updated Gauss2DCostSym to do the same as the new Gauss2DCost | 13 May 2014, 22:54:17 UTC |
| f3e6a7b | Stephanie Johnson | 13 May 2014, 22:50:48 UTC | Edited Fit2DGaussToSpot to work with the new Gauss2DCost, that is, to fit all or only some parameters | 13 May 2014, 22:50:48 UTC |
| bdaa280 | Stephanie Johnson | 13 May 2014, 22:09:00 UTC | Edited Gauss2DCost so that you can fit some or all parameters, not just all, and put a note in Fit2DGaussToSpot about why fminsearch is being used | 13 May 2014, 22:09:00 UTC |
| 9091499 | Stephanie Johnson | 01 May 2014, 18:25:34 UTC | Minor edits towards what I want to eventually do | 01 May 2014, 18:25:34 UTC |
| ea63253 | Stephanie Johnson | 30 April 2014, 17:36:35 UTC | Fully implemented the use of my new FRETmap class for analyzing DNAs also and not just doing the mapping | 30 April 2014, 17:36:35 UTC |
| a975993 | Stephanie Johnson | 30 April 2014, 00:07:53 UTC | Added functionality to check transform with extra bead movies | 30 April 2014, 00:07:53 UTC |
| e7c9043 | Stephanie Johnson | 28 April 2014, 23:57:08 UTC | Added functionality to channel mapping such that it redoes the trasformation till the residuals are below some threshold, also minor bug fixes | 28 April 2014, 23:57:08 UTC |
| 2f74ba7 | Stephanie Johnson | 25 April 2014, 23:56:38 UTC | Bug fixes in FindSpotMatches | 25 April 2014, 23:56:38 UTC |
| 8119780 | Stephanie Johnson | 25 April 2014, 17:06:58 UTC | Bug fixing | 25 April 2014, 17:06:58 UTC |
| f159c58 | Stephanie Johnson | 25 April 2014, 16:29:33 UTC | Added features to FRETmap class | 25 April 2014, 16:29:33 UTC |
| e02ce8a | Stephanie Johnson | 17 April 2014, 22:16:12 UTC | Added a FRETmap class for encapsulating channel mapping transformations | 17 April 2014, 22:16:12 UTC |
| e073fbb | Stephanie Johnson | 11 April 2014, 03:44:09 UTC | Finessed ScaleMovieV2 a bit, and added a way to load a previously done scaling | 11 April 2014, 03:44:09 UTC |
| e23e531 | Stephanie Johnson | 10 April 2014, 05:30:51 UTC | Fixed a bug with watching the movie with the traces | 10 April 2014, 05:30:51 UTC |
| a86cb5c | Stephanie Johnson | 10 April 2014, 05:00:04 UTC | Compared my results to IDL results, that weird intensity fluctuation is really there, so implemented the option of normalizing to each frame's median intensity. Traces totally smooth now | 10 April 2014, 05:00:04 UTC |
| 2c2e4ff | Stephanie Johnson | 06 April 2014, 17:45:06 UTC | Now scaling movie before finding spots and calculating their background. Unclear if it helped | 06 April 2014, 17:45:06 UTC |
| 5b86eb3 | Stephanie Johnson | 06 April 2014, 03:38:59 UTC | Error fixing, but I realized I did that wrong ... Need to scale movie first then find spots | 06 April 2014, 03:38:59 UTC |
| f919032 | Stephanie Johnson | 06 April 2014, 03:02:13 UTC | Added functionality to use backgrounds from gauss fit in intensity weighting | 06 April 2014, 03:02:13 UTC |
| 80a5276 | Stephanie Johnson | 05 April 2014, 04:13:56 UTC | one last minor edit | 05 April 2014, 04:13:56 UTC |
| 50509df | Stephanie Johnson | 05 April 2014, 04:11:28 UTC | Minor edits | 05 April 2014, 04:11:28 UTC |
| 36fc449 | Stephanie Johnson | 05 April 2014, 03:51:07 UTC | Added functionality to refine each found spot's center by a Gaussian, regardless of whether the user wants to weight by a Gaussian when calculating intensity | 05 April 2014, 03:51:07 UTC |
| 2fb3deb | Stephanie Johnson | 05 April 2014, 02:51:34 UTC | Minor changes | 05 April 2014, 02:51:34 UTC |
| 7687c53 | Stephanie Johnson | 05 April 2014, 01:38:54 UTC | Took out image scaling when playing movie | 05 April 2014, 01:38:54 UTC |
| f8543ec | Stephanie Johnson | 04 April 2014, 22:18:20 UTC | Added ability to watch movie during user analysis | 04 April 2014, 22:18:20 UTC |
| 00ce391 | Stephanie Johnson | 04 April 2014, 22:18:06 UTC | Integrated PlayMovie into UserSpotSelection and debugged. | 04 April 2014, 22:18:06 UTC |
| 26b7e19 | Stephanie Johnson | 04 April 2014, 16:13:17 UTC | Added functionality so that PlayMovie will play into the figure created by UserSpotSelection. Not yet debugged | 04 April 2014, 16:13:17 UTC |
| 801f877 | Stephanie Johnson | 03 April 2014, 20:02:33 UTC | Added a function that will play movie | 03 April 2014, 20:02:33 UTC |
| 94ba593 | Stephanie Johnson | 03 April 2014, 05:00:18 UTC | Created a function to load part of the scaled and background-subtracted movie | 03 April 2014, 05:00:18 UTC |
| b5b889c | Stephanie Johnson | 02 April 2014, 23:11:54 UTC | Added background subtraction for bead finding. Smoothing was worse than not smoothing for both beads and DNA | 02 April 2014, 23:11:54 UTC |
| f629f08 | Stephanie Johnson | 02 April 2014, 18:37:54 UTC | Minor changes to parameter settings | 02 April 2014, 18:37:54 UTC |
| 205ff18 | Stephanie Johnson | 29 March 2014, 23:51:25 UTC | Minor changes | 29 March 2014, 23:51:25 UTC |
| be40cef | Stephanie Johnson | 27 March 2014, 16:40:16 UTC | Minor bug fix | 27 March 2014, 16:40:16 UTC |
| b1b53df | Stephanie Johnson | 27 March 2014, 04:36:28 UTC | Minor bug fix | 27 March 2014, 04:36:28 UTC |
| 0ff00c5 | Stephanie Johnson | 27 March 2014, 04:29:10 UTC | Added a zoomed image of the spot; and now saves scaled, bkgnd subtracted movie frames | 27 March 2014, 04:29:10 UTC |
| c0abc77 | Stephanie Johnson | 27 March 2014, 02:58:33 UTC | Minor little improvements | 27 March 2014, 02:58:33 UTC |
| 0178456 | Stephanie Johnson | 20 March 2014, 03:01:30 UTC | Implemented background subtraction; background is subtracted as an average value every 100 frames | 20 March 2014, 03:01:30 UTC |
| ac63577 | Stephanie Johnson | 20 March 2014, 00:49:21 UTC | Oops forgot to be tracking a file for last commit; and attempted a background subtraction which did not work | 20 March 2014, 00:49:21 UTC |
| 2e5e4b6 | Stephanie Johnson | 19 March 2014, 23:10:47 UTC | Allow user to not Gaussian weight intensities | 19 March 2014, 23:10:47 UTC |
| d3d3761 | Stephanie Johnson | 19 March 2014, 22:22:39 UTC | Finished allowing user to decide whether to use composite image or separate channels to identify molecules | 19 March 2014, 22:22:39 UTC |
| 5086c55 | Stephanie Johnson | 19 March 2014, 21:08:56 UTC | Most of the way towards allowing user to choose to use a composite image or not | 19 March 2014, 21:08:56 UTC |
| 6c576a9 | Stephanie Johnson | 19 March 2014, 20:45:49 UTC | Part-way through allowing user to choose between using a combined image or using separate images | 19 March 2014, 20:45:49 UTC |
| 44831d1 | Stephanie Johnson | 19 March 2014, 20:35:44 UTC | GaussFitSpots had actually become my real working master, so branched master to OriginalWorkingVersion, and merged GaussFitSpots into master | 19 March 2014, 20:35:44 UTC |
| 200c943 | Stephanie Johnson | 19 March 2014, 20:34:57 UTC | Minor edits | 19 March 2014, 20:34:57 UTC |
| 6f3126c | Stephanie Johnson | 14 March 2014, 03:36:55 UTC | Minor bug fixes and edits | 14 March 2014, 03:36:55 UTC |
| 0f8dce6 | Stephanie Johnson | 08 March 2014, 01:50:34 UTC | Added background subtraction for real data | 08 March 2014, 01:50:34 UTC |
| 12d2b56 | Stephanie Johnson | 28 February 2014, 07:55:33 UTC | Switched to a polynomial transformation rather than affine, to see if I could recover FRETing spots. No luck yet | 28 February 2014, 07:55:33 UTC |
| b502fe0 | Stephanie Johnson | 28 February 2014, 01:51:49 UTC | Debugged last commit | 28 February 2014, 01:51:49 UTC |
| 796539b | Stephanie Johnson | 28 February 2014, 01:24:07 UTC | Integrated the new Gaussian-weighted intensity calculation into the whole code | 28 February 2014, 01:24:07 UTC |
| 4a27448 | Stephanie Johnson | 28 February 2014, 01:07:05 UTC | Wrote the code to weight each frame's intensity by a Gaussian | 28 February 2014, 01:07:05 UTC |
| ccf4b50 | Stephanie Johnson | 28 February 2014, 00:40:17 UTC | Mostly have the code working to fit a Gaussian to each intial spot, and decide whether the fit is better in the red or the green channel | 28 February 2014, 00:40:17 UTC |
| 9c2cf9e | Stephanie Johnson | 26 February 2014, 21:09:38 UTC | Whoops delinquent about commits, most of the way to an intensity calculation like the Ha lab IDL code | 26 February 2014, 21:09:38 UTC |
| fc60b7a | Stephanie Johnson | 22 February 2014, 05:23:52 UTC | Partway through integrating the GaussFit with real DNA spots into intensity calculation | 22 February 2014, 05:23:52 UTC |
| b87a742 | Stephanie Johnson | 22 February 2014, 03:25:24 UTC | Minor bug fixes | 22 February 2014, 03:25:24 UTC |
| 378b324 | Stephanie Johnson | 22 February 2014, 02:52:53 UTC | Found and fixed a bug in how spots were displayed mapped onto the image they were found in | 22 February 2014, 02:52:53 UTC |
| 9fd9a67 | Stephanie Johnson | 22 February 2014, 01:42:08 UTC | Can now decide between GaussFit refinement for beads in smFRETsetup, since I cant decide what is better right now | 22 February 2014, 01:42:08 UTC |
| 9440730 | Stephanie Johnson | 22 February 2014, 01:25:10 UTC | Minor edits to Fit2DGaussToSpot, so it does not display warnings if it does not converge | 22 February 2014, 01:25:10 UTC |
| 0e24018 | Stephanie Johnson | 22 February 2014, 00:32:09 UTC | Added option to refine spot centers by GaussFit. For beads increases computer time by 2x, minimal channel mapping improvement | 22 February 2014, 00:32:09 UTC |
| 29ba3b8 | Stephanie Johnson | 20 February 2014, 06:02:25 UTC | Debugged Gaussian fitting to spot; also added the option of fitting a symmetric Gaussian | 20 February 2014, 06:02:25 UTC |
| 68a2893 | Stephanie Johnson | 20 February 2014, 04:09:43 UTC | Reworked my old 2D Gaussian fitting code to fit a gaussian to an image of a spot | 20 February 2014, 04:09:43 UTC |
| fb594d6 | Stephanie Johnson | 20 February 2014, 02:44:53 UTC | Edits to readme | 20 February 2014, 02:44:53 UTC |
| 6e1e348 | Matthew Johnson | 11 February 2014, 21:11:24 UTC | fix more comments, c.f. #5 | 11 February 2014, 21:11:24 UTC |
| 27f12f1 | Matthew Johnson | 11 February 2014, 21:05:31 UTC | fix indented comments, c.f. #5 | 11 February 2014, 21:05:31 UTC |
| 202c018 | Stephanie Johnson | 11 February 2014, 20:30:00 UTC | One last addition to README to do list | 11 February 2014, 20:30:00 UTC |
| 4e04b6e | Stephanie Johnson | 11 February 2014, 20:19:27 UTC | Merge GitHub master branch, with Matt's changes to my commenting format, with my local master | 11 February 2014, 20:19:27 UTC |
| c26d2d4 | Stephanie Johnson | 11 February 2014, 20:17:57 UTC | Updated to do in README | 11 February 2014, 20:17:57 UTC |
| eb04470 | Stephanie Johnson | 11 February 2014, 20:08:42 UTC | Added information about the data repo | 11 February 2014, 20:08:42 UTC |
| 6d51809 | Stephanie Johnson | 11 February 2014, 16:49:33 UTC | Added financial support to acknowledgements | 11 February 2014, 16:49:33 UTC |
| 8dc27c2 | Stephanie Johnson | 11 February 2014, 00:44:20 UTC | Updated gitignore | 11 February 2014, 00:44:20 UTC |
| 9dc3670 | Stephanie Johnson | 11 February 2014, 00:28:36 UTC | Added a gitignore so it doesn't track the sample data | 11 February 2014, 00:28:36 UTC |
| dc16158 | Matthew Johnson | 11 February 2014, 00:26:45 UTC | re-apply #5 | 11 February 2014, 00:26:45 UTC |
| 6a9e0ae | Stephanie Johnson | 11 February 2014, 00:04:27 UTC | Manual merge github plus steph local master | 11 February 2014, 00:04:27 UTC |
| fe92249 | stephlj | 10 February 2014, 22:26:02 UTC | Merge pull request #5 from stephlj/mattjj/better-help-and-comments fix comment style | 10 February 2014, 22:26:02 UTC |
| 905bbfd | Matthew Johnson | 07 February 2014, 23:29:31 UTC | re-apply #1 | 07 February 2014, 23:31:24 UTC |
| 3cba58a | Matthew Johnson | 07 February 2014, 23:24:51 UTC | fix comment style | 07 February 2014, 23:24:51 UTC |
| 11dc887 | Stephanie Johnson | 07 February 2014, 17:04:39 UTC | Updated README to include an acknowledgements section | 07 February 2014, 17:04:39 UTC |
| c297eeb | Stephanie Johnson | 21 January 2014, 21:45:00 UTC | Added a function, ExamineChannelMap, that plots the difference between the output of CalcChannelMap versus FitGeoTrans. Unclear results | 21 January 2014, 21:45:00 UTC |
| 2253f96 | Stephanie Johnson | 21 January 2014, 20:34:17 UTC | Minor README typo fixes | 21 January 2014, 20:34:17 UTC |
| 2ebe50a | Stephanie Johnson | 18 January 2014, 00:45:03 UTC | Consistent use of double numeric type for right now | 18 January 2014, 00:45:03 UTC |
| 1dc0855 | Stephanie Johnson | 18 January 2014, 00:37:40 UTC | Merged the version of CalcSpotIntensityV2 that retains numeric type into this branch | 18 January 2014, 00:37:40 UTC |
| 06ceb0a | Stephanie Johnson | 18 January 2014, 00:31:28 UTC | Minor edits, had too many figures appearing and not getting closed | 18 January 2014, 00:31:28 UTC |
| 0df5a97 | Stephanie Johnson | 18 January 2014, 00:14:29 UTC | Since I can't decide between fitgeotrans and my CalcChannelMapping, right now it calculates and saves both | 18 January 2014, 00:14:29 UTC |
| 6b30dc7 | Stephanie Johnson | 17 January 2014, 23:07:30 UTC | Readme changes | 17 January 2014, 23:07:30 UTC |
| 6478404 | Stephanie Johnson | 17 January 2014, 23:01:42 UTC | More additions to README | 17 January 2014, 23:01:42 UTC |
| c5cb888 | Stephanie Johnson | 17 January 2014, 16:48:43 UTC | Minor README changes | 17 January 2014, 16:48:43 UTC |
| 57929c8 | Stephanie Johnson | 17 January 2014, 16:47:00 UTC | README changes | 17 January 2014, 16:47:00 UTC |
| cdf4559 | Stephanie Johnson | 17 January 2014, 16:44:25 UTC | Minor edits to README | 17 January 2014, 16:44:25 UTC |
| e9bc421 | Stephanie Johnson | 17 January 2014, 05:05:57 UTC | Ok just kidding now done with README | 17 January 2014, 05:05:57 UTC |
| 38e72f9 | Stephanie Johnson | 17 January 2014, 05:04:23 UTC | Finished README for now | 17 January 2014, 05:04:23 UTC |
