https://github.com/quantumjot/impy-tools
Additional tools for use with ImPy
https://github.com/quantumjot/impy-tools
Last synced: 3 months ago
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Additional tools for use with ImPy
- Host: GitHub
- URL: https://github.com/quantumjot/impy-tools
- Owner: quantumjot
- License: mit
- Created: 2015-06-16T18:26:33.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2018-03-31T16:13:26.000Z (about 7 years ago)
- Last Synced: 2025-01-12T23:43:46.713Z (4 months ago)
- Language: Python
- Size: 30.3 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# impy-tools
A set of tools for manipulating and converting data using ImageJ and MATLAB. These should be relatively
intuitive in their use.
## Functions/Loaders
+ MATLAB scripts and functions to manipulated Octopus data streams, or load single-molecule data from ThunderSTORM.
+ ImageJ (Python) plugins to import Octopus streams and create image datasets for machine learning.
## Notes
MATLAB scripts can be used as follows:
### OctopusLoader.m
A class for loading Octopus streams into MATLAB
```sh
% load the Octopus stream
OData = OctopusLoader('./SMLM/Calibration9_');
% grab frame 100
frame = OData.get_frame(100)
% grab the frame and header information
frame,header = OData.get_frame(100)
% grab only the header information
header = OData.get_header(100)
```
### ThunderSTORMLoader.m
A function to load exported ThunderSTORM localisation data into MATLAB. It should be agnostic as to the localisation
method used, and should label all headers correctly in the results table. Can be used as follows:
```sh
molecules = ThunderSTORMLoader('./SMLM/PALM_mEOS9M_.csv');
```