- data
- confocal.mat: original bacteria data
- latticeLightSheet.jpg: overexposed image of bacteria
- 3D.tif: 3D image of bacteria
- docs
- progress and final report for experiment
- images
- all saved output images of experiment
- Skeleton3D
- Courtesy of Philip Kollmannsberger
- Freely available on MathWorks File Exchange
- Calculates the 3D skeleton of an arbitrary binary volume using parallel medial axis thinning.
- Available here: https://www.mathworks.com/matlabcentral/fileexchange/43400-skeleton3d
- Used in process_3D to skeletonize 3D bacteria image
- process_*.m
- MATLAB files to process the three data files
- Shewanella_Bacteria_Counting_Report.pdf
- final report for this experiment
- Navigate to this folder in MATLAB
- Select all folders in this directory > Right Click > Add to Path > Selected Folders
- Run desired MATLAB file (comments within file may offer further instructions)
Read a summary of the results in Shewanella_Bacteria_Counting_Report.pdf in this repo