| 042fdd9 | xigumalu | 08 March 2016, 18:49:19 UTC | ops.mimg is concatenated mean images from blocks | 08 March 2016, 18:49:19 UTC |
| 049c170 | marius10p | 07 March 2016, 16:53:18 UTC | fixed mimg to be equal to mimg1 | 07 March 2016, 16:53:18 UTC |
| 049e168 | marius10p | 06 March 2016, 22:52:20 UTC | implemented non-rigid registration in interpolated blocks | 06 March 2016, 22:52:20 UTC |
| 1c3b25e | marius10p | 06 March 2016, 20:18:11 UTC | block registration, test 2 | 06 March 2016, 20:18:11 UTC |
| c8d19b2 | marius10p | 06 March 2016, 20:17:22 UTC | blocked registration, test commit | 06 March 2016, 20:17:22 UTC |
| 1fd7427 | marius10p | 06 March 2016, 16:38:04 UTC | Merge branch 'master' of https://github.com/cortex-lab/Suite2P | 06 March 2016, 16:38:04 UTC |
| 2110dce | marius10p | 06 March 2016, 16:36:24 UTC | released forced niterations in run_pipeline and removed master_fileMP.m | 06 March 2016, 16:36:24 UTC |
| a38bf40 | marius10p | 28 February 2016, 16:06:00 UTC | sdad | 28 February 2016, 16:06:00 UTC |
| 98aaf38 | marius10p | 21 February 2016, 16:38:24 UTC | updated NEU model extraction | 21 February 2016, 16:38:24 UTC |
| 2bcc7cd | xigumalu | 17 February 2016, 11:19:07 UTC | changed comments in master_file | 17 February 2016, 11:19:07 UTC |
| 881b21d | xigumalu | 17 February 2016, 10:57:34 UTC | Fixed neuropil calculation when all cells are considered | 17 February 2016, 10:57:34 UTC |
| ce1edf6 | xigumalu | 12 February 2016, 14:17:21 UTC | Deleted if clause | 12 February 2016, 14:17:21 UTC |
| 1aad88d | marius10p | 11 February 2016, 11:09:54 UTC | Update README.txt | 11 February 2016, 12:47:53 UTC |
| c10bdde | xigumalu | 11 February 2016, 09:53:42 UTC | Creates bin file of registered movie based on ops output from run_pipeline | 11 February 2016, 12:47:52 UTC |
| d07e927 | marius10p | 10 February 2016, 21:14:13 UTC | fixed bug | 11 February 2016, 12:47:52 UTC |
| 0e1f7e0 | marius10p | 10 February 2016, 16:13:49 UTC | fixed conflicts with how to run neuropil subtraction | 11 February 2016, 12:47:50 UTC |
| faf9e84 | marius10p | 10 February 2016, 15:56:33 UTC | new model for cell detection including neuropil can specify whether to use the new model or not (ops0.clustModel) and which neuropil method to use (surround as implemented by Mario, or the model-interpolated background) | 11 February 2016, 12:45:33 UTC |
| 852a81a | marius10p | 03 February 2016, 15:47:45 UTC | fixed save path for registered tiffs | 11 February 2016, 12:40:47 UTC |
| 5876138 | marius10p | 30 January 2016, 09:36:52 UTC | ops0.sig = 0 | 11 February 2016, 12:40:39 UTC |
| 7aa662b | xigumalu | 09 February 2016, 19:58:29 UTC | Bug fix (make compatible with gui2P) | 09 February 2016, 19:58:29 UTC |
| 954f0bd | xigumalu | 08 February 2016, 13:19:11 UTC | Check for empty ROI masks | 08 February 2016, 13:19:11 UTC |
| 25f1f99 | xigumalu | 05 February 2016, 11:57:24 UTC | Option to skip signal+neuropil calculation Also: description of parameters for get_signals_and_neuropil in master_file; option name changes in get_signals_and_neuropil | 05 February 2016, 11:57:24 UTC |
| f9ad900 | xigumalu | 04 February 2016, 18:23:53 UTC | Merge pull request #11 from marius10p/neuropil_SS Neuropil | 04 February 2016, 18:23:53 UTC |
| 54eb074 | xigumalu | 04 February 2016, 18:19:51 UTC | bug fixes + comments | 04 February 2016, 18:19:51 UTC |
| 672639f | xigumalu | 04 February 2016, 17:48:32 UTC | Merge remote-tracking branch 'refs/remotes/origin/master' into neuropil_SS | 04 February 2016, 17:48:32 UTC |
| 82808ca | xigumalu | 04 February 2016, 17:45:49 UTC | Makes neuropil calculation more flexible, more options | 04 February 2016, 17:45:49 UTC |
| abba00d | xigumalu | 03 February 2016, 11:34:22 UTC | Merge remote-tracking branch 'refs/remotes/origin/master' into neuropil_SS | 03 February 2016, 11:34:22 UTC |
| 2c6d7e1 | xigumalu | 02 February 2016, 17:35:05 UTC | Bug fixes in calculation of mean red image | 02 February 2016, 17:35:05 UTC |
| 248a385 | xigumalu | 02 February 2016, 11:32:09 UTC | Extract zoom factor from tiff header | 02 February 2016, 11:32:09 UTC |
| 02f204b | xigumalu | 01 February 2016, 20:12:03 UTC | includes all zoom factors + added Bergamo2 as scope type | 01 February 2016, 20:12:03 UTC |
| 6aa3af0 | xigumalu | 01 February 2016, 19:34:49 UTC | test commit | 01 February 2016, 19:34:49 UTC |
| a8c9e55 | xigumalu | 29 January 2016, 15:05:47 UTC | Bug fix | 29 January 2016, 15:05:47 UTC |
| 995ae77 | xigumalu | 29 January 2016, 11:21:27 UTC | Load red channel from local tiffs + check no. of frames matches no. of channels | 29 January 2016, 11:21:27 UTC |
| 5765c9e | MarioDipoppa | 26 January 2016, 14:19:38 UTC | Merge pull request #10 from marius10p/Suite2pMD Bugs fixed | 26 January 2016, 14:19:38 UTC |
| 2d67711 | MarioDipoppa | 26 January 2016, 14:14:59 UTC | Bug fixed run_pipeline has only three input variables | 26 January 2016, 14:14:59 UTC |
| 1158f9a | MarioDipoppa | 22 January 2016, 11:01:07 UTC | Add comments Comments on fixed variables that could become input parameters or read automatically from the file | 25 January 2016, 17:29:54 UTC |
| f45362c | marius10p | 21 January 2016, 10:12:50 UTC | Merge branch 'master' of https://github.com/marius10p/Suite2P | 21 January 2016, 10:12:50 UTC |
| 5e5b1da | marius10p | 21 January 2016, 10:12:05 UTC | Merge branch 'refs/heads/pr/7' | 21 January 2016, 10:12:05 UTC |
| 8cece98 | marius10p | 21 January 2016, 10:11:01 UTC | Merge remote-tracking branch 'refs/remotes/origin/master' into pr/7 | 21 January 2016, 10:11:01 UTC |
| a0376e4 | marius10p | 21 January 2016, 10:08:20 UTC | Merge pull request #7 from llerussell/master Fix: Undefined variable "img" or class "img.nFrames" | 21 January 2016, 10:08:20 UTC |
| 975aac3 | marius10p | 20 January 2016, 16:13:00 UTC | changes SVD decomposition from single to double Error code -12 with some nSVD when doing SVD !!!!!!!!!!!!! | 20 January 2016, 16:13:00 UTC |
| eb29d98 | marius10p | 15 January 2016, 19:03:45 UTC | uncomment function | 15 January 2016, 19:03:45 UTC |
| 589c0a6 | marius10p | 15 January 2016, 16:59:35 UTC | Merge remote-tracking branch 'origin/master' | 15 January 2016, 16:59:35 UTC |
| 97d6311 | marius10p | 15 January 2016, 16:56:48 UTC | NEW MASTER_FILE Necessary for new tiff loading function. Reduces number of options in both master_file and db variable. | 15 January 2016, 16:56:48 UTC |
| a7b18ee | marius10p | 15 January 2016, 16:54:09 UTC | Revert "NEW MASTER_FILE" This reverts commit 0f77449e90d24726ed3f620060750e3b31be4ba5. | 15 January 2016, 16:54:09 UTC |
| 0f77449 | marius10p | 15 January 2016, 16:53:48 UTC | NEW MASTER_FILE New and improved loading mechanism requires new master_file, reduces number of options in the header. Similarly reduces number of required options in db variable. | 15 January 2016, 16:53:48 UTC |
| c7245f1 | xigumalu | 15 January 2016, 16:16:34 UTC | bug | 15 January 2016, 16:16:34 UTC |
| e40295e | marius10p | 15 January 2016, 16:12:54 UTC | Merge remote-tracking branch 'origin/master' # Conflicts: # run_pipeline.m | 15 January 2016, 16:12:54 UTC |
| a79265e | marius10p | 15 January 2016, 16:10:29 UTC | update for faster reads from zserver + a few things Automatically determines the number of planes etc | 15 January 2016, 16:10:29 UTC |
| 11b59ae | Lloyd Russell | 13 January 2016, 15:27:46 UTC | Fix: Undefined variable "img" or class "img.nFrames" remove reference to nonexistent img object | 13 January 2016, 15:27:46 UTC |
| 146bfa8 | Lloyd Russell | 11 January 2016, 14:27:01 UTC | Merge remote-tracking branch 'marius10p/master' | 11 January 2016, 14:27:01 UTC |
| 5dcea89 | MarioDipoppa | 07 January 2016, 18:01:26 UTC | Cleaning up Clean up code | 07 January 2016, 18:01:26 UTC |
| 941e751 | MarioDipoppa | 07 January 2016, 17:59:10 UTC | Fixed bug on computing mean images New code do not assume that the tiff files are multiples of nPlanes*nChans | 07 January 2016, 17:59:10 UTC |
| 9906b9a | MarioDipoppa | 16 December 2015, 11:25:20 UTC | Two functions for neuropil infoPixUm: compute the ratio pixel/micrometers | 16 December 2015, 11:25:36 UTC |
| bdd8e0a | marius10p | 15 December 2015, 21:53:37 UTC | reverted run_pipeline to run without neuropil temporarily | 15 December 2015, 21:53:37 UTC |
| db51765 | marius10p | 15 December 2015, 15:30:15 UTC | adds red channel mean image to already processed data If you processed a dataset without getting mean image of the red channel (functionality not yet included as of 15/12/2015), then run "master_redAddon" to get the red mean image. | 15 December 2015, 15:30:15 UTC |
| f149b66 | MarioDipoppa | 15 December 2015, 13:23:06 UTC | Neuropil extraction Replaced get_signals with get_signals_and_neuropil | 15 December 2015, 13:23:06 UTC |
| 57a2d5d | MarioDipoppa | 15 December 2015, 13:16:00 UTC | Bug fixed Eliminated function overfprintf not available in +img | 15 December 2015, 13:16:00 UTC |
| 0d0dafb | MarioDipoppa | 15 December 2015, 13:14:30 UTC | Neuropil extraction Pipeline now computes neuropil Masks and extract the neuropil signal for post process of the data. The new variables are stat(k).ipix_neuropil for the mask and FcellNeu for the neuropil traces. | 15 December 2015, 13:14:30 UTC |
| 2db2676 | marius10p | 11 December 2015, 15:02:11 UTC | empty fields in db no longer overwrite fields in ops | 11 December 2015, 15:02:11 UTC |
| 6a60cac | marius10p | 11 December 2015, 11:51:33 UTC | added neuropil extraction Needs Mario to interface his neuropil masks function in. | 11 December 2015, 11:51:33 UTC |
| cbbe8ea | marius10p | 02 December 2015, 00:49:08 UTC | reverted the final output name to use specified number of clusters | 02 December 2015, 00:49:13 UTC |
| cf62e51 | sfailor | 01 December 2015, 18:55:33 UTC | Bug fixes | 01 December 2015, 18:55:33 UTC |
| c12012d | Lloyd Russell | 26 November 2015, 15:29:59 UTC | Merge remote-tracking branch 'marius10p/master' | 26 November 2015, 15:29:59 UTC |
| ccd1977 | sfailor | 24 November 2015, 17:41:46 UTC | mkdir bug fix Was checking for incorrect subdirectories and then creating them | 24 November 2015, 17:42:12 UTC |
| bad7030 | marius10p | 24 November 2015, 17:03:44 UTC | fixed bug due to new folder structure | 24 November 2015, 17:03:51 UTC |
| f9ff675 | Chris Burgess | 24 November 2015, 13:35:50 UTC | Improved options handling Implemented a getOr pattern for getting options with defaults. getOr can also take a cell array of option names so it can check for alternatives in case the names have changed. This pattern is now used in registation_offsets and translate_movie. TODO: implement substructure option referencing, as in getOr(ops, 'reg.phaseCorrelation', false) | 24 November 2015, 13:35:50 UTC |
| ee6587a | Chris Burgess | 24 November 2015, 12:38:51 UTC | Bugfixes and new translate_movie function Bugfix to registration_offsets on small batches Added preliminary translate_movie function ultimately intended to replace register_movie. - It can return the valid x and y indices over the whole movie given the translations to help with clipping the wrapped edges. - Works on batches of frames to help it run a bit faster, and you can safely run it on as many frames as you can fit in your system RAM. - Defaults to returning translated movie with same precision input movie. Do we need to be able to specify it? - Uses subpixel parameter to round translations appropriately. I suggest removing this function from registration_offsets so that always returns the most accurate offsets, which can be rounded later (during translation) if desired. | 24 November 2015, 12:38:51 UTC |
| 3dcd8c3 | Chris Burgess | 23 November 2015, 18:46:16 UTC | Improved registration accuracy and speed revamped registration_offsets (registration_offsets_old is bugfixed version of previous in case I broke anything). About twice as fast on GPU when registering at least 1000 frames. A little bit faster on CPU. More accurate (with phase correlation and subpixel) due to smoothing after whitening (and bugfixes). Adds an option for upsampling during registration for even more subpixel accuracy, but this is slower (about the same speed or slightly slower than the old function). Added this option to master_file. test_registration function compares the old and new registration functions for speed and accuracy by registering a randomly shifted frame registration_target tries to find the best target frame amongst a selection of frames by finding the frame with the highest peak phase correlation with every other frame. | 23 November 2015, 18:46:16 UTC |
| b306e66 | marius10p | 23 November 2015, 17:54:39 UTC | see new master_file.m | 23 November 2015, 17:54:39 UTC |
| c3cf3ae | marius10p | 23 November 2015, 17:23:16 UTC | added an intermediate folder made up of experiment numbers | 23 November 2015, 17:23:16 UTC |
| 7ed7c81 | marius10p | 23 November 2015, 13:31:49 UTC | added pixel-level correlation with secondary signal Allows pixel-level correlation maps to be computed from the SVD components. This is faster and more smooth than computing from raw pixel data. Uses precomputed SVD components saved by the pipeline. | 23 November 2015, 13:31:49 UTC |
| 0f3c6c3 | marius10p | 16 November 2015, 16:23:38 UTC | added SVD-based PixelMaps and whole GLM folder PixelMaps\example_PixelMapsSVD.m has a walkthrough with an example recording. Just plug in your own recording to get the same! | 16 November 2015, 16:23:38 UTC |
| 286f503 | marius10p | 16 November 2015, 13:37:29 UTC | switched to svd for low nSVD It seems to be faster than eigs for less than 1000 components or so, though I have not precisely measured. | 16 November 2015, 13:37:29 UTC |
| d59cce8 | marius10p | 09 November 2015, 18:04:20 UTC | fixed ranges of ichanrange It was not correctly aligning multi-plane data when registering tiffs with a number of frames non-divisible by the number of planes. | 09 November 2015, 18:04:25 UTC |
| f305650 | marius10p | 08 November 2015, 21:06:56 UTC | nimgbegend added as an option | 08 November 2015, 21:06:56 UTC |
| 0abff67 | marius10p | 07 November 2015, 14:10:19 UTC | added nimgbegend and single tiff file checks nimgbegend was not added as an option in the master file with the previous submission. The code was checking whether the folders were copied from zserver but not whether the files exist in the folders, now it is checking every single tif file. | 07 November 2015, 14:10:19 UTC |
| 5b0cfcb | marius10p | 04 November 2015, 19:33:05 UTC | removed keyboard | 04 November 2015, 19:33:05 UTC |
| e7ca1fb | marius10p | 04 November 2015, 19:07:41 UTC | added back tiff file writing writes tiff files in 2000 frame chunks. Added parameter nimgbegend which is the number of frames at the beginning and end of each experiment to average frames over. Result is saved in ops.mimg_beg and ops.mimg_end. This can be used to determine whether there was drift during the experiment. | 04 November 2015, 19:07:47 UTC |
| a79724a | xigumalu | 02 November 2015, 18:37:33 UTC | Fixed bug concerning registration with red channel | 02 November 2015, 18:37:49 UTC |
| d8b3779 | marius10p | 31 October 2015, 22:44:37 UTC | fixed ichanset range at pre-alignment | 31 October 2015, 22:44:37 UTC |
| 6141ccf | marius10p | 30 October 2015, 11:16:06 UTC | fixed red_align bug | 30 October 2015, 11:16:13 UTC |
| f28a791 | marius10p | 23 October 2015, 18:03:27 UTC | updated README file | 23 October 2015, 18:03:27 UTC |
| 38453cb | marius10p | 23 October 2015, 15:18:37 UTC | final master_file | 23 October 2015, 15:18:37 UTC |
| 45d2b24 | marius10p | 23 October 2015, 15:13:00 UTC | included db information in README file | 23 October 2015, 15:13:00 UTC |
| e7c0e45 | marius10p | 23 October 2015, 15:01:59 UTC | finished README.txt | 23 October 2015, 15:01:59 UTC |
| 5715ef1 | marius10p | 23 October 2015, 13:54:12 UTC | added tiff loading functions | 23 October 2015, 13:54:21 UTC |
| e47633f | marius10p | 22 October 2015, 16:39:57 UTC | added SfN poster Shows the pipeline in action for a project I am working on. | 22 October 2015, 16:39:57 UTC |
| 6cb5bd2 | marius10p | 22 October 2015, 16:30:05 UTC | readme | 22 October 2015, 16:30:13 UTC |
| 032145e | marius10p | 22 October 2015, 16:28:13 UTC | registration tweaks | 22 October 2015, 16:28:20 UTC |
| f649cc0 | marius10p | 22 October 2015, 16:08:36 UTC | general information in the README | 22 October 2015, 16:08:36 UTC |
| 02c1740 | marius10p | 22 October 2015, 15:40:21 UTC | added readme | 22 October 2015, 15:40:21 UTC |
| 55a8d55 | marius10p | 11 October 2015, 21:46:42 UTC | do not load ops from disk | 11 October 2015, 21:46:42 UTC |
| a466eea | marius10p | 11 October 2015, 21:15:45 UTC | fixed reg2Pnew for single plane the parallel loading of planes and squeezing was not working for single plane. | 11 October 2015, 21:15:45 UTC |
| 7b8db16 | marius10p | 11 October 2015, 08:45:14 UTC | updates to work fast on Michael's data - changed the logic of the filepaths to allow multiple animal names. Local copy merges experiments under the first animal name specified. - registration works simultaneously on all planes so that each tiff can be deleted after processing. Requirement on hard drive reduced to total size of acquired data. This is the best we can do because the bin files need to be stored at this size anyway. - fixed registration instability issue: it was related to the local center of mass using negative values of the correlation, which could cancel out with the peak and result in a near-zero mass which was used in a denominator. - fixed ROI detection to split all ROIs into connected pieces, not just the ones satisfying criteria. - added to each region's stat the number of its parent, so that statistics of the parent can be computed post-hoc. - | 11 October 2015, 08:45:14 UTC |
| 40bd115 | marius10p | 10 October 2015, 21:08:05 UTC | fixed first cycle issues Fixed reg2P issues, but not SVD issues. In the short term it doesn't really matter because the first frames are a small percentage of all frames/ | 10 October 2015, 21:08:05 UTC |
| 33ad4c2 | marius10p | 09 October 2015, 20:59:47 UTC | missing cell detection functions added | 09 October 2015, 20:59:47 UTC |
| bbe3f02 | mkrumin | 09 October 2015, 12:25:27 UTC | MINOR: avoiding a 'not integer' warning array index needs to be an integer | 09 October 2015, 12:25:27 UTC |
| fac5312 | marius10p | 08 October 2015, 14:25:43 UTC | swapped rmdir for delete function of individual tiff files | 08 October 2015, 14:25:43 UTC |
| 294a3f2 | marius10p | 08 October 2015, 14:07:21 UTC | copy data locally now fixed build_ops was not returning file paths for temporarily copied tiffs. | 08 October 2015, 14:07:21 UTC |
