mitocheck_movies

All information regarding the download and processing of Mitocheck whole movies from IDR study with accession idr0013 (screenA) (paper, data, metadata). Scripts used to download movies were modified from mitocheck_data and scripts used for illumination correction were modified from the preprocessing step of IDR_stream. Movies are downloaded with Aspera using download.py. Note that the full dataset is > 20 TB so the number of plates to download should be specified by changing the plate_subset variable. Then illumination correction is performed with PyBaSiC and imageJ using either process_single_movie.py or process_multiple_plates.py. You can change the number of frames to include in the shortened video using the frames variable and you can control the image compression using the down_factor variable. Once processed, movies will appear with the same name and save path as the original movie but saved with the extension .avi.

Aspera Downloader:

Step 1: Install Aspera

Install Aspera high-speed transfer client as described here. We used the direct installation method. On Ubuntu, the direct installation method is as follows:

1. Install Ruby on Ubuntu: sudo apt install ruby-full
2. Confirm Ruby install: ruby --version
3. Install aspera-cli gem: gem install aspera-cli
4. Upgrade aspera-cli gem to latest version: gem update aspera-cli
5. Install acsp: ascli conf ascp install
6. Confirm install and locate acsp (for step 1a): ascli config ascp show

Step 1a: Allow Aspera to run without password

It is necessary to allow Aspera command line interface (ascp) to run without your system password to use it more easily with python. In order to run ascp without a password do the following:

1. Type sudo visudo at the terminal to open the sudo permissions (sudoers) file
2. Find the line with: %sudo ALL=(ALL:ALL) ALL
3. Below that line, insert the following line: username ALL=(ALL) NOPASSWD: path_to_aspera Note: username is your username and path_to_aspera can be found with ascli config ascp show
4. Save and exit the editor

Step 2: Download Aspera Public Key

Download and Aspera public key. You will need the location of this key to use Aspera

Image Processing

Step 1: Install Fiji

Download the version of Fiji (ImageJ) compatible with your system. Fiji is used to open images.

Step 2: Install PyImageJ

PyImageJ is the python wrapper function for ImageJ.

Step 3: Install PyBaSic

PyBaSiC is used to perform illumination correction.