Quick Start

Quick Start #


Installation
These instructions do not currently work because the source code is in private repositories. As soon as we publish and the source code is released this page will be functional.

Installation #

This software can be deployed on any machine, as long as Docker is preinstalled, however it is recommended to deploy on a cloud server.

The setup below if for a public instance, not password protected. Password protection is possible through a slightly more involved installation process that will be added.

The easiest approach is to use a Digital Ocean droplet, but any web hosting platform can be used if you have a particular preference. If you have said preference I will assume you can modify the instructions below to work for you, if you have never set up a remote server before then just follow the instructions below.

Digital Ocean Droplet #

  1. Create an account on Digital Ocean.
  2. Create a new droplet.
  3. For image select Docker from the Marketplace tab.
  4. For plan select any, all will work but higher cores will be faster.
  5. Under additional options select User data. Copy and past the following bash script.
    #!/bin/bash
    wget https://gitlab.com/hect-software/rianu/-/raw/main/docker-compose.yml -P /root/
    docker-compose -f /root/docker-compose.yml up -d
    
  6. Set authentication. Preferably with SSH keys however if you don’t know what those are just set a password. These will only be used if you need to SSH into the machine, this will not be used to access the web interface.
  7. Create the droplet. This will take ~5 mins to fully set up. Just because it gives an ip address does not mean it has finished installing.
  8. Access the droplet via http://<IP-OF-DROPLET>/. If it does not resolve it means it has not finished installing so just wait a few more minutes.

Build from Source #

If the Docker images are not working you can build from source. This can either be done on a local machine or by SSHing into a remote machine. This approach assumes some experience with the command line.

  1. Clone this repository on the machine you want to run it on.
  2. CD into the root of the project.
  3. Build from source using this command.
    docker-compose -f docker-compose-build.yml up -d
    
  4. Access via web browser. If on local machine, http://localhost/. If on a server http://<IP-OF-SERVER>/.

Experiment Setup #

Once the droplet is set up you can access Rianú via http://<IP-OF-SERVER>/.

Before uploading videos you should set up your environment. Go to the database page.

  1. Create a new experiment. You can choose what you want this to mean, but essentially an experiment is just a folder you use to group related videos.
  2. Add all the bioreactors you plan to use with information about post heights, tissue heights, etc.

Video Upload #

Once you have your experiments and bioreactors set up you can start uploading videos. Go to the upload page.

  1. Select date recorded, which bioreactor it is in, and which experiment it is part of from dropdowns.
  2. Click to blue plus button to add as many tissues as are in the video you are uploading.
  3. For each tissue select which post it is on from the dropdown, and enter tissue number and type.
  4. Input the frequency this video was paced at, if spontaneous I usually just put 0.
  5. Add a video note, this will show up in the database to help you remember what is happening in this video.
  6. Upload a video and submit, you should be redirected to the database page.

Video Tracking #

To track a video that has been uploaded go to the database page.

  1. Select the experiment from the Videos section below the experiments and bioreactors.
  2. The videos with greyed out Analyze buttons have not been tracked yet, find the one you want and click Track. You will be redirected to a new page.
  3. Calibrate the video. You have three options on how to do this.
    1. Calibration set: If already calibrated a different video you can select that same calibration factor.
    2. Calibration factor: If you analyzed the video in different software and have a calibration factor you can add it here. It should be in px/mm.
    3. Calibration distance: You can draw a box of a known length on the video to calibrate. First enter the known distance in mm, then draw a box on the frame. The diagonal of the box between the first and second click will be taken and used to calculate the calibration factor.
  4. Draw tissue widths. Draw a box for each tissue the length of its cross-section. The diagonal of the box between the first and second click will be used.
  5. Draw the post starting locations. Draw a box around each post. Here are a few important notes about his process.
    1. The first click should be the top left corner and the second the bottom right, after the first click when you move your mouse you can see what the box looks like before confirming with the second click.
    2. Tissues should be selected in the order they were entered on the upload.
    3. Posts should be selected so the first post draw for each tissue corresponds to the left post entered in the bioreactor.
  6. Once the last post is selected the tracking will automatically start in the background. The Analyze button on the database page will turn blue once it has finished tracking and is ready for analysis. Tracking will usually take under 5 minutes, but it really depends on length of video, FPS, number of tissues being tracked, and how powerful the computer is.

Video: Tracking Demo. Calibration box (black), tissue cross sections (pink), and starting post locations (red) annotated.


Tissue Analysis #

  1. You can either perform analysis by:
    • Each tissue: Below the videos in an experiment there is a dropdown with numbers. Select the number for the tissue you want to analyze. Analysis will be performed on that tissue for every video it is in.
    • Each video: Click analyze next to the video you want to analyze, it will perform analysis on all tissues present in that video
  2. If there are no graphs just refresh the page. If the graphs do not automatically have peaks and points that means is couldn’t find any peaks. Try these fixes.
    1. Lower the threshold value
    2. Lower the minimum distance slider
  3. Adjust the smoothing and point finding parameters until you agree with the points being found for each tissue.
    • Polynomial (default: 3): Lower is smootherumentation
    • Window Size (default: 13): Higher is smoother.
    • Prominence (Default: .5): Decrease if it is not finding peaks (by amplitude).
    • Minimum Distance (default: 15): Increase to skip peaks (by time).
    • Buffer (default: 15): Increase if finding basepoints of frontpoints before it should.
    • Inverse (default: off): Inverts the raw data.
    • Detrend (default: off): Finds a removes a linear trend from the data.
  4. Once you are happy with all the points, click Calculate at the top of the page. A csv will be downloaded with twitch parameters for all tissues analyzed.

Experiment Archival #

When an experiment has concluded a zip of that experiement can be downloaded from the database page. The zip contains all videos, bioreactor metadata, post location data, and twitch parameters. The experiment can then be deleted off the server and the zip stored offline wherever the user likes. If the would ever like to re-analyze that data they can go to the upload page and upload the entire zip.