83a0b5f | Kai Wohlfahrt | 01 August 2016, 10:35:57 UTC | Factor out binning | 01 August 2016, 10:35:57 UTC |
3e7c3e5 | Kai Wohlfahrt | 31 July 2016, 18:40:11 UTC | Plot survival time of molecules Plots a decay curve of molecules with lifetime > than a given number. | 31 July 2016, 18:40:11 UTC |
b2c1379 | Kai Wohlfahrt | 27 July 2016, 15:57:52 UTC | Make median-filter length variable | 27 July 2016, 15:57:52 UTC |
d204b61 | Kai Wohlfahrt | 27 July 2016, 15:31:07 UTC | Use subplots instead of add_subplot | 27 July 2016, 15:31:07 UTC |
14f6254 | Kai Wohlfahrt | 27 July 2016, 15:30:35 UTC | Show total number of traces analyzed | 27 July 2016, 15:30:35 UTC |
be43081 | Kai Wohlfahrt | 26 July 2016, 13:04:43 UTC | Use nearest interpolation for extract plot | 26 July 2016, 13:25:34 UTC |
dd5a755 | Kai Wohlfahrt | 26 July 2016, 13:02:46 UTC | Add another dataset | 26 July 2016, 13:25:29 UTC |
216123f | Kai Wohlfahrt | 25 July 2016, 15:22:51 UTC | Add another dataset | 25 July 2016, 15:23:24 UTC |
3dc46da | Kai Wohlfahrt | 25 July 2016, 15:06:53 UTC | Handle 1-sample case roundMean failed because no variance available (i.e. log10 failed). | 25 July 2016, 15:06:53 UTC |
7026e9d | Kai Wohlfahrt | 07 July 2016, 12:58:52 UTC | Add power dependency samples to extract.fish | 07 July 2016, 13:04:27 UTC |
ec13e3b | Kai Wohlfahrt | 07 July 2016, 12:58:24 UTC | Add binning to fret analysis | 07 July 2016, 13:04:27 UTC |
a398dd7 | Kai Wohlfahrt | 06 July 2016, 11:53:00 UTC | Add poisson HMM Adds an initial poisson-based HMM. Test for a further expansion to simulate CCD (poisson photon count + multiplier + gaussian noise). Also includes some simple code to demonstrate hmmlearn. | 06 July 2016, 15:36:26 UTC |
9032521 | Kai Wohlfahrt | 04 July 2016, 09:47:52 UTC | Round mean/variation to correct significant figs | 04 July 2016, 09:47:52 UTC |
8cab0d6 | Kai Wohlfahrt | 04 July 2016, 09:47:35 UTC | Plot mean/variation lines | 04 July 2016, 09:47:35 UTC |
0012cfb | Kai Wohlfahrt | 04 July 2016, 09:46:36 UTC | Add padding to sample plot Matplotlib was cutting off first few pixels, which caused a few things to apparently have no spots. | 04 July 2016, 09:46:36 UTC |
40fbb01 | Kai Wohlfahrt | 04 July 2016, 09:46:01 UTC | Exclude dataset from extraction Has y-axis drift | 04 July 2016, 09:46:01 UTC |
218b5cc | Kai Wohlfahrt | 04 July 2016, 09:45:34 UTC | Explicitly specify params in extraction script Don't rely on defaults, might change accidentally. | 04 July 2016, 09:45:34 UTC |
e7ad0cf | Kai Wohlfahrt | 04 July 2016, 09:41:25 UTC | Use halfway point as threshold Same as done by Steve's program. | 04 July 2016, 09:41:25 UTC |
7c7af27 | Kai Wohlfahrt | 01 July 2016, 15:41:42 UTC | Test array path for excludeFrames | 01 July 2016, 15:41:42 UTC |
7df0c15 | Kai Wohlfahrt | 01 July 2016, 12:59:50 UTC | Add plotting to extract.py | 01 July 2016, 15:39:27 UTC |
043d12a | Kai Wohlfahrt | 01 July 2016, 11:24:26 UTC | Add peakEnclosed test for arrays | 01 July 2016, 15:39:27 UTC |
dd83628 | Kai Wohlfahrt | 30 June 2016, 20:10:33 UTC | Add extract for iterables | 01 July 2016, 15:39:26 UTC |
cda7683 | Kai Wohlfahrt | 30 June 2016, 16:49:17 UTC | Remove unused argument | 01 July 2016, 15:39:25 UTC |
3ded372 | Kai Wohlfahrt | 30 June 2016, 16:48:42 UTC | Add excludeFrames for iterable sequence | 01 July 2016, 15:39:24 UTC |
b6a4da4 | Kai Wohlfahrt | 30 June 2016, 15:45:44 UTC | Add 561 dataset to extract.fish | 30 June 2016, 16:30:20 UTC |
52d8ceb | Kai Wohlfahrt | 30 June 2016, 15:45:02 UTC | Make extract normalization optional Later data-sets have no background variance. | 30 June 2016, 16:30:20 UTC |
b327694 | Kai Wohlfahrt | 30 June 2016, 14:38:04 UTC | Crop samples symmetrically | 30 June 2016, 14:38:04 UTC |
9f810a3 | Kai Wohlfahrt | 29 June 2016, 16:21:10 UTC | Use fwd + backward derivative for laplacian This makes the picked points better centered on the source points. | 29 June 2016, 16:21:10 UTC |
bad571d | Kai Wohlfahrt | 29 June 2016, 16:20:41 UTC | Improve blob.py plotting | 29 June 2016, 16:20:41 UTC |
0af46a4 | Kai Wohlfahrt | 21 June 2016, 09:15:20 UTC | Use mean instead of max per frame Should give better signal/noise. Also reduce the sampling area. | 21 June 2016, 09:15:20 UTC |
61f05c8 | Kai Wohlfahrt | 21 June 2016, 09:12:55 UTC | Add pickle format for blob.py output | 21 June 2016, 09:12:55 UTC |
0444c79 | Kai Wohlfahrt | 20 June 2016, 10:20:35 UTC | Move analyze.fish -> extract.fish | 20 June 2016, 10:20:35 UTC |
48c389b | Kai Wohlfahrt | 13 June 2016, 13:10:04 UTC | Extract raw frames Extracts raw frames (instead of median-filtered), and allows for excluding frame ranges at the extraction level. This makes further processing a bit more flexible. | 13 June 2016, 13:10:04 UTC |
8d99b66 | Kai Wohlfahrt | 09 June 2016, 11:23:02 UTC | Improve blob.py command line Adds plotting and CSV writing (as opposed to print). | 09 June 2016, 11:23:02 UTC |
3779e95 | Kai Wohlfahrt | 03 June 2016, 14:20:38 UTC | Update blob.py as executable Prints coordinates from an image passed on the command line, instead of a fixed demo. | 03 June 2016, 14:20:38 UTC |
ace0531 | Kai Wohlfahrt | 02 June 2016, 14:54:48 UTC | Fix sphere intersection Intersection only valid if volumes actually intersect and d != 0, so check for this. Clamp all other values to 0 (not strictly correct for d == 0). | 02 June 2016, 14:54:48 UTC |
12130f1 | Kai Wohlfahrt | 27 May 2016, 10:02:15 UTC | Load traces on demand, keep only stats | 27 May 2016, 10:02:15 UTC |
55c08bf | Kai Wohlfahrt | 27 May 2016, 10:00:41 UTC | Pad sample if rows cannot be factorized | 27 May 2016, 10:00:41 UTC |
e9cff56 | Kai Wohlfahrt | 22 May 2016, 22:34:03 UTC | Compare multiple datasets in analysis Nested dicts are a little awkward to work with. Maybe time to consider SQL? | 22 May 2016, 22:34:03 UTC |
1d451cd | Kai Wohlfahrt | 22 May 2016, 21:36:36 UTC | Rework stat organization Organize into dict to keep title and stat together. | 22 May 2016, 21:36:36 UTC |
2de74f0 | Kai Wohlfahrt | 22 May 2016, 21:22:09 UTC | Split out sampling code Removes randomness from remaining analysis. Also aims are a little different, sampling randomly from multiple different experiments doesn't make much sense. | 22 May 2016, 21:23:22 UTC |
0d529bd | Kai Wohlfahrt | 22 May 2016, 19:34:57 UTC | Add analysis of multiple repeats to fret_analysis Analyses multiple repeats and returns std deviation between repeats in summary statistics. | 22 May 2016, 19:34:57 UTC |
e34c276 | Kai Wohlfahrt | 22 May 2016, 16:59:15 UTC | Add analysis script Finds series of TIF images per dataset & video in specified directories, and extracts ROIs by calling extract.py | 22 May 2016, 16:59:15 UTC |
a2a2d79 | Kai Wohlfahrt | 22 May 2016, 12:04:41 UTC | Support multi-file series Adds tiffConcat to concatenate multiple TIFF files in a memory-efficient manner. | 22 May 2016, 12:04:41 UTC |
04d718b | Kai Wohlfahrt | 20 May 2016, 10:56:49 UTC | Split ROI extraction and plotting Question is where to plot selected peaks. Data is available in extraction. | 20 May 2016, 10:56:49 UTC |
091717e | Kai Wohlfahrt | 19 May 2016, 12:10:55 UTC | Reorganize stat collection Fixes photons/frame (previously was photons/blink/on time). Also reorganizes other functions to be clearer, though possibly slower. | 19 May 2016, 14:19:48 UTC |
bc2db39 | Kai Wohlfahrt | 19 May 2016, 11:00:09 UTC | Process multiple files This adds processing of multiple datasets. Removes plotting of selected samples on projection for convenience. TODO: - Compute standard deviation between datasets, not between all data points. - Restore plotting of collected samples on projection. | 19 May 2016, 11:00:09 UTC |
b6f188f | Kai Wohlfahrt | 18 May 2016, 14:59:40 UTC | Move output argument Preparation for accepting multiple image series | 18 May 2016, 14:59:40 UTC |
f4da1d9 | Kai Wohlfahrt | 18 May 2016, 14:59:18 UTC | Clean up numpy imports | 18 May 2016, 14:59:18 UTC |
51eb8bb | Kai Wohlfahrt | 18 May 2016, 14:47:29 UTC | Output summary statistics Print summary statistics to csv/stdout | 18 May 2016, 14:47:29 UTC |
1368fd3 | Kai Wohlfahrt | 18 May 2016, 11:17:25 UTC | Add .gitignore | 18 May 2016, 11:17:25 UTC |
135b888 | Kai Wohlfahrt | 18 May 2016, 11:16:08 UTC | Add photon count / frame | 18 May 2016, 11:16:08 UTC |
79b5752 | Kai Wohlfahrt | 17 May 2016, 14:07:37 UTC | Add png output Currently all plots are the same (~A4) size, can adjust. | 17 May 2016, 14:07:37 UTC |
2410e15 | Kai Wohlfahrt | 17 May 2016, 13:27:33 UTC | Count truncated last blink Last blink is always included in the photon count, so also include it in the blink count even if it is truncated. | 17 May 2016, 13:28:05 UTC |
bb1cf60 | Kai Wohlfahrt | 17 May 2016, 13:26:48 UTC | Parallelize rollingMedian Biggest time taken here, so use parallel map. | 17 May 2016, 13:26:48 UTC |
072450c | Kai Wohlfahrt | 17 May 2016, 13:25:40 UTC | Limit histogram bins Limit largest bin to 95th percentile, reduces compression of data by outliers. | 17 May 2016, 13:25:40 UTC |
e0da62f | Kai Wohlfahrt | 17 May 2016, 12:25:02 UTC | Add per-blink photon counts | 17 May 2016, 12:25:02 UTC |
2de233b | Kai Wohlfahrt | 17 May 2016, 11:24:46 UTC | Add total photon count | 17 May 2016, 11:24:46 UTC |
11122fa | Kai Wohlfahrt | 17 May 2016, 09:34:10 UTC | Add blink counts Note on-state must be signed int for gradient extraction to work. | 17 May 2016, 10:39:27 UTC |
96ccd67 | Kai Wohlfahrt | 17 May 2016, 09:33:21 UTC | Use single level threshold for on/off | 17 May 2016, 09:33:21 UTC |
abcf3c6 | Kai Wohlfahrt | 17 May 2016, 09:25:21 UTC | Pre-calculate traces/rois, index for samples All ROIs and traces will be needed anyway (ROIs for photon count later). This allows marking the sampled regions in the projection. | 17 May 2016, 09:25:21 UTC |
9247de8 | Kai Wohlfahrt | 16 May 2016, 15:13:53 UTC | Make seed parameter for sample selection explicit | 16 May 2016, 15:17:44 UTC |
0a52e66 | Kai Wohlfahrt | 13 May 2016, 10:17:40 UTC | Use indices.stop to get subplot dims | 13 May 2016, 10:17:40 UTC |
6671c96 | Kai Wohlfahrt | 12 May 2016, 17:08:15 UTC | Pre-filter entire image Applies a median blur to the entire image before spot picking. Reduces number of spurious spots. | 12 May 2016, 17:08:15 UTC |
71945f7 | Kai Wohlfahrt | 12 May 2016, 16:13:31 UTC | Divide by pre-computed background | 12 May 2016, 16:13:31 UTC |
e425e61 | Kai Wohlfahrt | 09 May 2016, 14:24:16 UTC | Display histogram of on-times and blink lengths | 09 May 2016, 14:52:15 UTC |
b94f66d | Kai Wohlfahrt | 09 May 2016, 14:24:07 UTC | Round ROI size to int 'scale' is np.int64, so cast to python int for round to work correctly. | 09 May 2016, 14:51:55 UTC |
3df297d | Kai Wohlfahrt | 09 May 2016, 14:20:04 UTC | Color lines by on/off state Slightly complicated with matplotlib, need to use LineCollection. http://matplotlib.org/examples/pylab_examples/multicolored_line.html | 09 May 2016, 14:20:04 UTC |
8ef27a8 | Kai Wohlfahrt | 05 May 2016, 10:19:03 UTC | Initial commit blob.py does Laplacian of Gaussian detection of blobs in nD data extract.py extracts spots from well-separated, static point sources, and plots their on/off state. | 05 May 2016, 10:19:03 UTC |