Commit 0c28fceb authored by Anders Sejr Hansen's avatar Anders Sejr Hansen

update

parent c2127e38
......@@ -2,6 +2,8 @@
% written by Anders Sejr Hansen (AndersSejrHansen@post.harvard.edu;
% @Anders_S_Hansen; https://anderssejrhansen.wordpress.com)
% License: GNU GPL v3
% Dependent functions:
% - RemoveAmbigiousTracks.m
clear; clc; close all;
% add path for dependent functions:
addpath('Functions');
......
......@@ -17,29 +17,30 @@ scales.
cells
1. Open script `MergeQC_SPT_data.m` and click run.
2. Use the script to merge data from multiple cells. Dependent
function:
function: `RemoveAmbigiousTracks.m`
3. Adjust `ClosestDist` to set the threshold in micrometers for
when particles are too close and trajectories should be aborted.
3.
3.
Update 2017-07-26
## Detailed description of each step
Below we will describe each step in more details.
Fixed plotting issue on small screen. Enabled weighting: if
UseWeights=1, Spot-On will now weigh each histogram at each dT
according to the relative amount of data in the least-squares
fitting.
#### Step 1 - Obtain SPT data at multiple temporal scales
Here we will use the provided example data for U2OS C32 Halo-hCTCF, which is provided in the directory `UnProcessedExampleData` and contains data at 3 frame rates: ~223 Hz, ~133 Hz, ~74 Hz.
#### Step 2 - Merge and QC the SPT data from many different single cells
When performing tracking and localization, each single cell results in
a single file. Thus, to keep things manageable, we use
`MergeQC_SPT_data.m` to merge data from all these single cells (~20-30
cells) into a single file for a given frame rate, by concatenating the
frames (e.g. if two movies with 20,000 frames are merged, frame 1 in
the second movie becomes frame 20,001). To minimize tracking errors,
we also use `ClosestDist = 2` (in units of μm) to abort trajectories
where two particles came closer than 2 μm to each other. This is
achieved by calling the function `RemoveAmbigiousTracks.m`.
Update 2018-02-02 version 1.04
The variable controlling whether all displacements from all
trajectories will be used has been renamed. "UseAllTraj" is now called
"UseEntireTraj" based on user feedback that the original name was
confusing. We would like to clarify that all trajectories are always
used, but that UseEntireTraj controls whether all displacements from a
given trajectory is used (yes if =1, no if =0).
Also improved plotting and performance. Compiling histograms is now
about 30-40% faster.
## Author
The code was written by and is maintained by Anders Sejr Hansen:
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