| f840f9c | Stephanie Johnson | 02 April 2019, 22:08:33 UTC | Added some input error handling for finding bead files to make channel maps | 02 April 2019, 22:08:33 UTC |
| 9324d33 | Stephanie Johnson | 29 March 2019, 00:49:44 UTC | Fixed a bug that would not let different movies in the same data set have different analysis parameters or different fps | 29 March 2019, 00:49:44 UTC |
| c2e82bc | Stephanie Johnson | 28 December 2018, 18:13:42 UTC | Minor change for backwards compatibility with old data | 28 December 2018, 18:13:42 UTC |
| 8744f9e | Stephanie Johnson | 14 December 2018, 05:17:39 UTC | Edit to README figure | 14 December 2018, 05:17:39 UTC |
| d9fb512 | Stephanie Johnson | 14 December 2018, 05:06:54 UTC | Resized README figure | 14 December 2018, 05:06:54 UTC |
| 7d984f4 | Stephanie Johnson | 14 December 2018, 05:03:39 UTC | Resized README figure | 14 December 2018, 05:03:39 UTC |
| de1b625 | Stephanie Johnson | 14 December 2018, 05:02:17 UTC | Trying to get README figure size right | 14 December 2018, 05:02:17 UTC |
| 3ca74af | Stephanie Johnson | 14 December 2018, 05:01:36 UTC | Removed figure from README | 14 December 2018, 05:01:36 UTC |
| c668447 | Stephanie Johnson | 14 December 2018, 05:00:50 UTC | Resized figure in README | 14 December 2018, 05:00:50 UTC |
| 0e5d783 | Stephanie Johnson | 14 December 2018, 04:59:48 UTC | Resized figure in README | 14 December 2018, 04:59:48 UTC |
| 8f0b321 | Stephanie Johnson | 14 December 2018, 04:58:50 UTC | Added figure to README | 14 December 2018, 04:58:50 UTC |
| bbcddf7 | Stephanie Johnson | 14 December 2018, 04:54:03 UTC | updated README to link to Slopey | 14 December 2018, 04:54:03 UTC |
| 0ced375 | Stephanie Johnson | 14 December 2018, 00:08:47 UTC | Fixed another problem with R2017a and later involving calls to ginput followed by calls to gca | 14 December 2018, 00:08:47 UTC |
| 760244f | Stephanie Johnson | 13 December 2018, 03:55:12 UTC | Final bug fixes to the decision of whether to use FRETmap or FRETmapR2017a with newer versions of matlab | 13 December 2018, 03:55:12 UTC |
| 4fc37f8 | Stephanie Johnson | 13 December 2018, 01:59:32 UTC | Debugged new FRETmapR2017a class and its integration into Traces | 13 December 2018, 01:59:32 UTC |
| eba0a52 | Stephanie Johnson | 13 December 2018, 00:29:22 UTC | Edited functions that call FRETmap constructor function to use new whichPoly field in params to pick which FRETmap class to use | 13 December 2018, 00:29:22 UTC |
| dac2cab | Stephanie Johnson | 12 December 2018, 22:30:10 UTC | Wrote a new class FRETmapR2017a that works with Matlabs changes to fitgeotrans and related functions, and code in Traces to check which version to use | 12 December 2018, 22:30:10 UTC |
| c74ea02 | Stephanie Johnson | 10 December 2018, 06:05:41 UTC | For R2017a and later, changed the use of keyboard to input for routine user input | 10 December 2018, 06:05:41 UTC |
| c65f021 | Stephanie Johnson | 04 December 2018, 01:46:56 UTC | Minor edits to README | 04 December 2018, 01:46:56 UTC |
| 241fdce | Stephanie Johnson | 04 December 2018, 01:41:18 UTC | Major edits to Manual for clarity | 04 December 2018, 01:41:18 UTC |
| aa30080 | Stephanie Johnson | 30 November 2018, 22:19:06 UTC | Added some lines to TracesSetup for handling new imshow default image size in R2017 | 30 November 2018, 22:19:06 UTC |
| a970e42 | Stephanie Johnson | 29 November 2018, 18:26:00 UTC | Supressed warning when using my custom polynomial transform calculation code | 29 November 2018, 18:26:00 UTC |
| b0b5bc6 | Stephanie Johnson | 24 November 2018, 23:54:55 UTC | Edited LoadScaledMovie to re-calculate background images if I'm reanalyzing an old data set | 24 November 2018, 23:54:55 UTC |
| 355dd81 | Stephanie Johnson | 12 April 2018, 21:11:42 UTC | Minor change to GUI plotting | 12 April 2018, 21:11:42 UTC |
| e1983a8 | Stephanie Johnson | 08 April 2018, 22:44:34 UTC | Updated Manual to indicate known bug with using MatlabPoly with R2017a and later | 08 April 2018, 22:44:34 UTC |
| bfdc7ba | Stephanie Johnson | 08 April 2018, 22:04:00 UTC | Bug fix to bug fix for setting TransformToCalc in TracesSetup to Poly | 08 April 2018, 22:04:00 UTC |
| 0158fff | Stephanie Johnson | 08 April 2018, 21:56:41 UTC | Bug fix for setting TransformToCalc in TracesSetup to Poly | 08 April 2018, 21:56:41 UTC |
| d161665 | Stephanie Johnson | 02 April 2018, 16:39:46 UTC | Added DOI to Readme | 02 April 2018, 16:39:46 UTC |
| a9d4fac | Stephanie Johnson | 21 February 2018, 16:30:56 UTC | minor changes to README | 21 February 2018, 16:30:56 UTC |
| 1ac1303 | Stephanie Johnson | 02 January 2018, 20:24:29 UTC | typo fix in UserSpotSelection | 02 January 2018, 20:24:29 UTC |
| 190de36 | Stephanie Johnson | 29 July 2017, 01:13:43 UTC | Fixed manual now that I have moved TracesSetup to the SampleFiles directory | 29 July 2017, 01:13:43 UTC |
| 203f478 | Stephanie Johnson | 18 July 2017, 21:16:31 UTC | Minor changes as the sample repo is added | 18 July 2017, 21:16:31 UTC |
| b913a28 | Stephanie Johnson | 16 July 2017, 21:56:33 UTC | Additional edits to manual based on adding sample data and making sure it executes | 16 July 2017, 21:56:33 UTC |
| 6fa6be1 | Stephanie Johnson | 16 July 2017, 21:47:51 UTC | Fixed some parts of the manual and pyhsmm subdir as I got the pyhsmm sampel data ready in the TracesSampleData repo | 16 July 2017, 21:47:51 UTC |
| 7b46aa6 | Stephanie Johnson | 16 July 2017, 20:24:37 UTC | Fixed a bug where you could not load old spots if SpotsAndIntensities had not been generated | 16 July 2017, 20:24:37 UTC |
| 680a527 | Stephanie Johnson | 16 July 2017, 20:02:40 UTC | Changed name of sample data repo in Traces Readme | 16 July 2017, 20:02:40 UTC |
| a5b4787 | Stephanie Johnson | 09 July 2017, 00:21:33 UTC | Minor readme fixes | 09 July 2017, 00:21:33 UTC |
| 3454b5f | Stephanie Johnson | 15 May 2017, 15:11:12 UTC | Updated TracesSetup to accurately reflect the way I now use ManualInjectMark | 15 May 2017, 15:11:12 UTC |
| 5064c39 | Stephanie Johnson | 22 March 2017, 03:41:54 UTC | Updated readme to render properly with CommonMark | 22 March 2017, 03:41:54 UTC |
| b0ed764 | Stephanie Johnson | 11 February 2017, 01:46:35 UTC | Bug fix to last commit | 11 February 2017, 01:46:35 UTC |
| eae3aa4 | Stephanie Johnson | 09 February 2017, 18:30:51 UTC | Added a debug param so that FindRefinedSpotCenters doesnt output failure modes unless asked, eg by UserSpotSelection | 09 February 2017, 18:30:51 UTC |
| f8903c5 | Stephanie Johnson | 25 January 2017, 22:54:06 UTC | Fixed language of residuals in manual | 25 January 2017, 22:54:06 UTC |
| c393bbf | Stephanie Johnson | 25 January 2017, 00:49:48 UTC | Uncommented the reporting outputs in FindRefinedSpotCenters so that the user is told why a spot cant be re-localized | 25 January 2017, 00:49:48 UTC |
| b4ac172 | Stephanie Johnson | 25 January 2017, 00:34:48 UTC | Changed UserSpotSelection to confirm that the user wants to quit if there are re-mapped spots still in the queue | 25 January 2017, 00:34:48 UTC |
| c2eae75 | Stephanie Johnson | 25 January 2017, 00:03:49 UTC | Fixed bug in UserSpotSelection where it would crash if you selected a region outside the bounds of the figure | 25 January 2017, 00:03:49 UTC |
| 9746ce8 | Stephanie Johnson | 23 January 2017, 17:47:55 UTC | Minor readme changes | 23 January 2017, 17:47:55 UTC |
| 2ed3ed1 | Stephanie Johnson | 23 January 2017, 06:17:13 UTC | Cleaned up the sample TracesSetup file, and cleaned up README | 23 January 2017, 06:17:13 UTC |
| fe6ca55 | Stephanie Johnson | 23 January 2017, 02:43:38 UTC | Updated manual to reflect the change to TracesSetup being in the SampleFiles directory | 23 January 2017, 02:43:38 UTC |
| 742001d | Stephanie Johnson | 23 January 2017, 02:40:06 UTC | Tracking the new directory SampleFiles | 23 January 2017, 02:40:06 UTC |
| 2ee02f6 | Stephanie Johnson | 23 January 2017, 02:38:33 UTC | Moved TracesSetup to the directory with the sample identity channel map, and changed the name of the directory to SampleFiles | 23 January 2017, 02:38:33 UTC |
| c20b1a9 | Stephanie Johnson | 23 January 2017, 02:37:19 UTC | Removed files generated by my tests | 23 January 2017, 02:37:19 UTC |
| 4ea13f3 | Stephanie Johnson | 23 January 2017, 02:35:57 UTC | Updated gitignore to ignore files generated while I was testing pyhsmm, and to exclude my personal TracesSetup file | 23 January 2017, 02:35:57 UTC |
| 90b788f | Stephanie Johnson | 23 January 2017, 02:31:46 UTC | Changed name of pyhsmm subdir to be less confusing | 23 January 2017, 02:31:46 UTC |
| 745e76a | Stephanie Johnson | 23 January 2017, 02:31:22 UTC | Updated manual to include pyhsmm info | 23 January 2017, 02:31:22 UTC |
| a18273e | Stephanie Johnson | 22 January 2017, 00:39:16 UTC | Minor modifications to ExamineHMMresults so its slightly less dumb, and halfway done updating manual with pyhsmm info | 22 January 2017, 00:39:16 UTC |
| 3ea5c5f | Stephanie Johnson | 21 January 2017, 18:10:52 UTC | Add pyhsmm to Traces | 21 January 2017, 18:10:52 UTC |
| 576dfe1 | Stephanie Johnson | 14 December 2016, 01:58:03 UTC | Updated readme | 14 December 2016, 01:58:03 UTC |
| 54a9f5e | Stephanie Johnson | 01 December 2016, 15:49:10 UTC | Changed DetectRedFlash to make it so that users can manually input flash locations if they werent automatically detected | 01 December 2016, 15:49:10 UTC |
| 2c34f65 | Stephanie Johnson | 16 September 2016, 18:38:32 UTC | Updated Traces manual to reflect compatibility with new versions of Micro-Manager | 16 September 2016, 18:38:32 UTC |
| 290a33a | Stephanie Johnson | 16 September 2016, 18:27:35 UTC | Whoops forgot to make the bead map section also compatible with new uManager, fixed that | 16 September 2016, 18:27:35 UTC |
| cbf4234 | Stephanie Johnson | 16 September 2016, 01:29:07 UTC | Made Traces compatible with the new uManager directory structure, did not update manual yet | 16 September 2016, 01:29:07 UTC |
| af7f18f | Stephanie Johnson | 26 July 2016, 00:32:16 UTC | More debugging | 26 July 2016, 00:32:16 UTC |
| f726c03 | Stephanie Johnson | 25 July 2016, 18:25:43 UTC | Debugging new traces xlim scaling | 25 July 2016, 18:25:43 UTC |
| 0da573f | Stephanie Johnson | 25 July 2016, 18:09:01 UTC | UserSpotSelection now always scales traces to the number of frames by default instead of whatever matlab thinks is best which often is terrible | 25 July 2016, 18:09:01 UTC |
| d529092 | Stephanie Johnson | 19 June 2016, 15:17:48 UTC | Now saving spotfinding thresholds in SpotsFound file | 19 June 2016, 15:17:48 UTC |
| 9c39b22 | Stephanie Johnson | 19 June 2016, 00:24:12 UTC | Now red flashes are saved in Scaling Info not params | 19 June 2016, 00:24:12 UTC |
| 29e9b68 | Stephanie Johnson | 18 June 2016, 16:44:27 UTC | Debug ScaleMovie changes | 18 June 2016, 16:44:27 UTC |
| ea4c908 | Stephanie Johnson | 18 June 2016, 02:03:52 UTC | Cleaned up a little | 18 June 2016, 02:03:52 UTC |
| 2892467 | Stephanie Johnson | 18 June 2016, 01:43:51 UTC | Now saving InjectPoints in ScalingInfo, and reorganizing ScaleMovie so its not such a mess | 18 June 2016, 01:43:51 UTC |
| 97ea206 | Stephanie Johnson | 18 June 2016, 00:50:22 UTC | no actual changes | 18 June 2016, 00:50:22 UTC |
| 499439a | Stephanie Johnson | 18 March 2016, 00:02:07 UTC | Fixing stuff | 18 March 2016, 00:02:07 UTC |
| 9483802 | Stephanie Johnson | 01 December 2015, 03:17:53 UTC | more readme edits | 01 December 2015, 03:17:53 UTC |
| 91e86f9 | Stephanie Johnson | 01 December 2015, 03:14:49 UTC | more readme edits | 01 December 2015, 03:14:49 UTC |
| a3c91d7 | Stephanie Johnson | 01 December 2015, 03:12:53 UTC | typo correct | 01 December 2015, 03:12:53 UTC |
| 628f398 | Stephanie Johnson | 01 December 2015, 03:10:03 UTC | Updated Readme and manual to match, and for Readme to make reference to iSMS | 01 December 2015, 03:10:03 UTC |
| 6ea486d | Stephanie Johnson | 30 November 2015, 01:15:29 UTC | Updated everything to use the new fps which is actually fps and not fpms | 30 November 2015, 01:15:29 UTC |
| 191b0c9 | Stephanie Johnson | 30 November 2015, 01:03:12 UTC | Traces manual and sample metadata file updated to reflect fps changes | 30 November 2015, 01:03:12 UTC |
| db8e8aa | Stephanie Johnson | 30 November 2015, 00:32:19 UTC | Changed GetInfoFromMetaData to use Andor-ActualInterval rather than Interval, and changed it to output a parameter that is truly fps, to fix that bad nomenclature. Now need to update every function that thinks fps is 1/fpms | 30 November 2015, 00:32:19 UTC |
| 24f3070 | Stephanie Johnson | 30 November 2015, 00:04:23 UTC | Update TracesSetup with new Tinj based on recalculation of frame rate | 30 November 2015, 00:04:23 UTC |
| 32639e7 | Stephanie Johnson | 07 August 2015, 00:28:33 UTC | Minor changes | 07 August 2015, 00:28:33 UTC |
| fdff639 | Stephanie Johnson | 30 June 2015, 03:47:47 UTC | More changes to Manual, and readme | 30 June 2015, 03:47:47 UTC |
| 87a6ba4 | Stephanie Johnson | 30 June 2015, 00:41:03 UTC | Made manual less stupid | 30 June 2015, 00:41:03 UTC |
| 7b601e0 | Stephanie Johnson | 29 June 2015, 23:35:43 UTC | small changes | 29 June 2015, 23:35:43 UTC |
| 09d9a6b | Stephanie Johnson | 29 April 2015, 16:53:35 UTC | Updated manual to reflect changes | 29 April 2015, 16:53:35 UTC |
| acf2863 | Stephanie Johnson | 29 April 2015, 16:12:53 UTC | Debugged | 29 April 2015, 16:12:53 UTC |
| f6d24f2 | Stephanie Johnson | 28 April 2015, 18:13:25 UTC | Added criteria that a red laser flash shows no spike in the green channel | 28 April 2015, 18:13:25 UTC |
| 4ad79c9 | Stephanie Johnson | 28 April 2015, 17:00:50 UTC | Debugging DetectRedFlash with stuff that starts in low FRET | 28 April 2015, 17:00:50 UTC |
| 360c38b | Stephanie Johnson | 28 April 2015, 15:47:03 UTC | Whoops forgot to commit the DetectRedFlash code last time, and here also integrated it into the rest of Traces | 28 April 2015, 15:47:03 UTC |
| 164f4f0 | Stephanie Johnson | 28 April 2015, 00:52:03 UTC | Implemented a detection algorithm for fiducial markers in red channel | 28 April 2015, 00:52:03 UTC |
| a482f5d | Stephanie Johnson | 27 April 2015, 21:21:52 UTC | small changes | 27 April 2015, 21:21:52 UTC |
| b803f98 | Stephanie Johnson | 19 April 2015, 04:13:58 UTC | Moved LoadUManagerTiffsV5 to tools, even though the manual lists it as pink not yellow, life goes on, its really both | 19 April 2015, 04:13:58 UTC |
| e0831bb | Stephanie Johnson | 19 April 2015, 03:09:19 UTC | Fixed bug #9 about the command key crashing UserSpotSelection | 19 April 2015, 03:09:19 UTC |
| 36d8362 | Stephanie Johnson | 18 April 2015, 22:50:25 UTC | last set I think of name change thingies | 18 April 2015, 22:50:25 UTC |
| c4814f9 | Stephanie Johnson | 18 April 2015, 22:49:47 UTC | oops more name change fixing | 18 April 2015, 22:49:47 UTC |
| e5d6154 | Stephanie Johnson | 18 April 2015, 22:46:51 UTC | Updated git ignore with name change, oops | 18 April 2015, 22:46:51 UTC |
| fa31ed1 | Stephanie Johnson | 18 April 2015, 22:24:20 UTC | Merged name change branch into my master branch | 18 April 2015, 22:24:20 UTC |
| 2556eda | Stephanie Johnson | 18 April 2015, 22:23:27 UTC | Updated Readme with name change and sales pitch for Traces | 18 April 2015, 22:23:27 UTC |
| c91a79b | Stephanie Johnson | 18 April 2015, 22:03:03 UTC | Updated manual to reflect the name change | 18 April 2015, 22:03:03 UTC |
| 2a2d4b4 | Stephanie Johnson | 18 April 2015, 21:49:57 UTC | Renamed smFRET to Traces and smFRETsetup to TracesSetup | 18 April 2015, 21:49:57 UTC |
| bb756f2 | Stephanie Johnson | 18 April 2015, 21:41:12 UTC | Organized everything into subdirectories and updated gitignore | 18 April 2015, 21:41:12 UTC |
