biointernship

A collection of the workflows and projects completed during my 2020 BioTrain Internship in Dr. Alex Harkess' Lab.

Any scripts ending in .py can be run over a directory of images.

A renaming script is available that will name all output images after their input image.

1. Initialize docker using terminal window (see initializedocker).

2. Open Jupyter notebook and start one Terminal tab and one Python 3 tab.

3. In the Python 3 tab, run OpenCV code to extract the individual frames from timelapse video (see vidtoframes).

4. Run any PlantCV workflow over image set while simultaneously creating a unique output file for each image (see initializedocker).

5. Run bash script to rename all output images after their unique frame (see rename-script.sh).

6. Use desktop terminal window (instead of the Jupyter notebook terminal tab) to copy your specific output images to a new directory (see intializedocker).

7. Sort images sequentially in directory (see initializedocker).

8. Copy and paste this sequential list into a .txt file, save in the directory you're in.

9. Using the dependency imagemagick in the desktop terminal window, run $ convert @step8.txt anyname.gif