make_video_from_images

This repository makes a video, with optional time stamp, from µManager time lapse image output.

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Contents

make_video_from_images.py
Use this script to make a video from µManager time lapse output.

make_video_from_images.py
    -i <input_image_dir>
    -o <output_image_dir>
    -t # Flag to include timestamp
    -z <interval_in_ms> # Only used if -t present, interval between images
    -s <buffer_in_s> # Only used if -t present, time from start to first frame

Requirements

pillow
ffmpeg-python
numpy

Example installation and use with Conda, rclone/Google Drive.

Setting up an environment

conda create -n make_video_from_images python=3.9 ffmpeg ffmpeg-python numpy pillow

Downloading files from Google Drive with rclone

rclone copy gdrive_me:/Imaging_videos_hypoploids/2021_zip_files_not_processed . --drive-shared-with-me -v

Unzipping the files

7za x '*.zip'

Running for a single folder of images
Note: not having a slash for the output directory is important, it makes the output video name with os.path.basename, which will return an empty string if there's a trailing slash.

conda activate make_video_from_images
python ~/scripts/make_video_from_images/python/make_video_from_images.py -i /xdisk/rpalaniv/cedar/images_to_videos/20210304/2_17_2021_5/Default/ -o /xdisk/rpalaniv/cedar/images_to_videos/20210304/2_17_2021_5 -t -z 500 -s 840

Putting all the videos in a single folder

find . -name '*.mp4' -exec mv {} /folder/path/ \;