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7. Image reconstruction
The parameters for lifetime augmentation are stored in the 'FLImBrushDataProcessingTool\ImageReconstruction\overlay_animation_spie19-bwformat\plotConfig.csv' file.
The best parameter setting will depend on the tissue type and scanning speed. Please play with it and update the parameter to fit your project.
The parameters are the following:
- LifetimeChannel --> channel to plot
- PlotRedox? --> whether to plot redox ratio or lifetime
- SNRLowerBound --> lower bound of SNR filter, if data SNR is lower than this, it will be removed
- CircleRadius --> Radius of FLIm overlay circle
- CircleOpacity --> transparency of the FLIm data circle
- LTCh1ColorScaleFrom --> channel 1 colorbar lower limit
- LTCh1ColorScaleTo --> channel 1 colorbar upper limit
- LTCh2ColorScaleFrom --> channel 2 colorbar lower limit
- LTCh2ColorScaleTo --> channel 2 colorbar upper limit
- LTCh3ColorScaleFrom --> channel 3 colorbar lower limit
- LTCh3ColorScaleTo --> channel 3 colorbar upper limit
- RedoxColorScaleFrom --> Redox ratio colorbar lower limit
- RedoxColorScaleTo --> Redox ratio colorbar upper limit
The file 'ImageReconstruction.m' is used to generate the augmented FLIm images.
File needed for reconstruction are the following, each from the specific run you would like to process:
- Decon data file --> deconvolved data file from the run you want to reconstruct. (.mat)
- CNN segementation file --> output of the CNN segmentation Python code. (.mat)
- txt file --> txt output file from the aquisition software. Stored in the folder 'txt' under data folder. (.txt)
- Video file --> un-augemented video file. (.avi)
After making sure you got all the required files, simply run 'ImageReconstruction.m', selecting the input files and wait :p. The output .jpg file will be in the same folder as the deconvolved data file.
The output of the file should look like the following.
