This tool is designed to analyse bottom and lateral videos. Analysis for bottom videos include speed, acceleration and cadence profiles. For lateral videos, we provide stick plots and angles analysis between different joints. The pose estimation is performed by DeepLabCut.
- Start by loading the appropriate conda environment. You do this by typing in 'conda activate DLC-CPU'
- Go into the directory in which "gait_analysis" tool is located.
- Start up the tool by typing 'python -m gait_analysis'
You will land on the main page of our tool. From here you can decide if you wish to start a new project, load an existing one or just perform a group analysis.
IMPORTANT!!!
In order to load a project, it must be structured (files names) in a way that our tool does it. This is imperative for the tool to work properly. The structure of a project directory looks like that:
Additionally, you can select which type of video you wish to analyse. The tool provides an option to either:
- only analyse bottom videos
- only analyse lateral videos
- analyse noth types of videos at the same time
IMPORTANT!!!
The tool makes a distinction between bottom and lateral videos based on the names of the file. Therefore it is crucial to keep a partical nomenclature. The difference for the corresponding bottom and lateral videos lies in the 'SIDEVIEW' prefix in the name of file. Example:
- Bottom video filename: Cage1_0L0R_20cms_0degUP_4.avi
- Lateral video filename: SIDEVIEW_Cage1_0L0R_20cms_0degUP_4.avi
The following demo shows the case where one selects to analyse combined videos. The same applies to all other options however this is the most general version.
If you decide to start a new project, the first thing to do is to specify where we want to create it. Simply press the 'Browse' button and select a directory in which new project should be created. Next you need to set the 'Project name' and 'Author name'. The full name of the project folder will comprise of the project name, author name and current date. Example:
Such parameters will create a project named 'Kiehn_Lab-test-2021-04-14'. In case where you already a project withthat name, the program will ask you if you whish to overwrite already existing project. BE CAREFUL WITH THIS!
In the next step you need to upload the video which are to be analysed. It is important to upload correct videos under specific name, therefore under 'bottom videos' upload bottom videos and the same for lateral. If by any chance you upload wrong videos do not worry! Simply press a 'RESET VIDEOS' button which will reset all uploaded videos and you can repeat the process.
Finally, you have an optional choice do save labeled videos with overlayed markers on the analysed videos. This option serves only visualisation purpose, where you can make sure, that the model predicted correctly.
In order to start the analysis press the 'RUN' button. A window will pop up telling how long the analysis is taking. When it disapears, this means that the analysis is finished. Corresponding labels will be save in a directory called 'Labels'.
IMPORTANT!!!
In case of loading an existing project, this step is ommited!!!
For the analysis of the bottom videos we provide 3 types of profiling: *Speed profile - showing the belt speed, avg.speed and avg. instantenous speed with its error over the whole video *Acceleration profile - showing instantenous acceleration and if existing, drag and recovery events over the whole video *Cadence profile - showing cadence and circular plots for selected limb coordination
We provide multiple optional choices, that are up to the user. Firstly, one has an option to decide, which plots should be included in the final pdf. This choices are represented by the following windows:
If you wish to include speed and acceleration profiles in your final pdf you simply must choose option 'Yes' in the corresponding box. This procedure is a bit different for the cadence profiles. You need to select which limb coordination you wish to include. In case of all of them being needed, simply mark 'Select all'.
Additionally, you have an option to save all the important parameters from the analysis as a csv/Excel table.
TREADMILL PARAMETERS
Regarding belt parameters, you have an option to specify these too. By defualt, we assume that the length of the treadmill is 20 cm however, if that is not the case, you can specify the length. Similar goes for the treadmill speed. By default, the tool assumes the speed from the name of the video file however, if the actuall speed was different, you can specify that too. If you wish to personalise both feature, simply check the corresponding checkbox and set the values in the following windows:
SPEED PROFILE PARAMETERS
For the speed profile plot, you can specify the 'noise filter'. This parameter smoothes out the plot and removes big variations, allowing for a good looking plot. By default it is set to 10, which is the value that we propose.
ACCELERATION PROFILES
In this part of the analysis you have a power over the selection of drag and recovery events. You need to choose a maximum time duration (in seconds) for the program to select steps during which recover/drag event occured. This steps will later on be eliminated from the analysis. The will also be plot on the acceleration profile plot with blue line for recovery event and red line for drag event.
In regards to lateral videos analysis, the only 2 options that the user can personalise is a scaling parameter for the stick plots and optional 'temporal synchronisation'. The following examples show the differences between those options.
As seen in the above comparison, the higher the scaling parameter the more tightly packed are the sticks in the plots becoming thiner.
Temporal synchronisation allows for analysis of differences in time of swing and stand phases.
IMPORTANT!!! TEMPORAL SYNCHRONISATION IS NOT YET AVAILABLE, BUT IT WILL BE FIXED SOON!
The process of working with already existing project is basically the same as when creating a new one. We skip the part in which we perform pose estimation and go straight to analysis of the coordinates. The only difference between loading and starting a project is one line on top of the screen:
In this window you can select where your project is located. Simply find your project directory and select it. Now, the tool knows which coordinates and videos to use and you can continue with the analysis.
The last part of the analysis that the tool provides, is the group analysis. This feature is only applicable to BOTTOM VIEW videos, as it groups the results of cadence profiles and checks if their differences are significant.
The main idea behind this analysis is the custom division of available videos, into maximum of 4 groups. The selection and naming of the groups is ultimately up to the user. As a result, the tool, creates a circular plot for each of the selected limb coordinations. Created circular plot included a mean vector for each of the created groups.
You can add videos to certain groups by clicking on the corresponding button on the right side of the group's name.
IMPORTANT!!! Selected videos have to be taken out of the project folder. We assume that the location of the videos is within a project structure and by following specific instruction the tool can find coresponding files with the coordinates.
Finally, you have the possibility to perform statistical analysis between selected groups. For this purpose the tool allows multiple personalised options that you can select from.
In order to allows for fair comparison we take particular amount of steps sampled from the pull. You can specify the type of the sampling and number of steps. If the selected number is mote then available, the tool will take the maximum amount of steps available.
IMPORTANT!!! The selection of all types of sampling is not yet implemented however it will be fixed soon!
For the statistical test, the tool provides two of them: *Watson-Williams test *Modified Rayleigh test
There is one more additional parameter called 'phi threshold' which is set to 0.5. this value describes how much do want the angles between the limbs to differ and not be eliminated from the analysis. We introduced this parameter as the markers could rarely be misplaced by the model during pose estimation. This is a quick fix to overcome such issue.
Finally you can select for which limb coordination you want to perform group analysis.
All of the produced results are stored with the project structure. The results comprised of: *Every plot that the user chose to create during the analysis - stored in the folder called 'allProfiles' *Optional csv table for Speed/Acceleration/Cadence profiles - called 'speedProfile.csv' and stored in the main project folder *Csv table with combined parameters including bottom and lateral videos (If there are both types of videos for the same animal) - called 'statistics.csv' and stored in the main project folder *Txt table with results of statistical testing during group analysis; includes the limb coordination, groups combination, type of test, p-value and significancy - called 'stats.txt' and stored in the main project folder
