Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ghosted syllables #214

Open
espy1412 opened this issue Feb 2, 2022 · 3 comments
Open

Ghosted syllables #214

espy1412 opened this issue Feb 2, 2022 · 3 comments
Labels
bug Something isn't working

Comments

@espy1412
Copy link

espy1412 commented Feb 2, 2022

Expected Behavior

In most syllables, the entire figure of the mouse appears.

Current Behavior

In a few syllables (some restricted to particular animals/conditions), a dark spot appears over the centroid of the animal in the crowd movies. There are other syllables that are whole. I have no idea whether these are being analyzed properly, though I assume so. What is more concerning are the syllables that look like faint rims of color and do not move very much.

Possible Solution

Well, I already faced the possibility that this was an analysis artifact when I recorded at the wrong height. Now that I am recording at the height of 685 mm and this type of problem persists, however, I think there is something else going on.

Steps to Reproduce (for bugs)

  1. Run "MoSeq2-Extract-Modeling-Notebook"
  2. Run "MoSeq2-Analysis-Visualization-Notebook"
  3. Examine crowd movies

Screenshots

Examples of moderate and severe ghosting are below.

syllable_sorted-id-43_.usage._original-id-83.mp4
syllable_sorted-id-60_.usage._original-id-73.mp4

Context

Ideally, I want to be able to prevent these types of syllables from being extracted, since they do not appear to be representative of the actual movement pattern of the mouse. It is unclear how to do that, though.

Your Environment

  • Version/GitHub branch used: v1.0.2beta/release
  • Device: Dell XPS 8940 (desktop, Intel 10900K, RTX 2070 SUPER)
  • OS: Windows 10
  • Link to your project:
syllable_sorted-id-43_.usage._original-id-83.mp4
syllable_sorted-id-60_.usage._original-id-73.mp4
@espy1412 espy1412 added the bug Something isn't working label Feb 2, 2022
@wingillis
Copy link
Collaborator

Hi @espy1412. Typically, if a mouse doesn't move for a majority of the session, its body will contaminate the background image, as the background image is computed using a sample of frames across the session. Have you looked at the background images generated by MoSeq for these extractions? You will likely see the body of the mouse present in the background image. Also, I'd expect that these dark spots also show up in the extraction videos.

The simplest workaround is to use the plane background parameter when computing the background image for these sessions. It fits a plane to the floor and removes the mouse's influence on computing the background image

@espy1412
Copy link
Author

espy1412 commented Feb 3, 2022

  1. Where is the place to examine the background image? I am assuming you are talking about the bground.tiff file that shows up in the proc subdirectory for each analyzed session? If so, I took a look at a few of these and did not see anything that looked like an animal's body.

  2. Are there any instructions for how exactly to "use the plane background parameter"? Is that a particular line in the notebooks or a modifiable variable?

Thanks!

@jonahpearl
Copy link

Did this get resolved? For the tiff files, to see such a slight variation in the background, you might have to load it in and mess with the colorscale. The way it gets saved, a difference of a few mm in the background would be hard to pick up.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

3 participants