Regions of Interest Feature

[2909ft]

Hello everybody! I have a minor question: there is a feature on the PrepareJAABAData interface which I am not entirely sure what it is used for (see attached image). Would it be possible to use this "regions of interest" feature to limit a specific behavior to happen only inside a certain ROI? (e.g.: every time the mouse is inside the ROI, the assigned behavior is always "Investigating"). If not, what is this feature used for? I couldn't find any information about it on the JAABA website.

Thank you for your time!

[mkabra]

Hi,

The Regions of Interest (ROI) is a limited functionality feature and that's why it isn't documented. Currently, if you specify a single ROI for CTrax, JCTrax or Two-Fly Tracker and JAABA will compute additional features: Distance to ROI and angle between animal's head direction and the line joining the center of the animal and the ROI. This can definitely be useful for behaviors like investigating where JAABA can potentially learn to predict investigating whenever the animal's distance is smaller than a threshold.

What tracker are you currently using? MoTR? It should be relatively easy to add single ROI features for MoTR trackers if that would be helpful.

Mayank

On Tue, Nov 12, 2019 at 1:40 PM 2909ft notifications@github.com wrote:

Hello everybody! I have a minor question: there is a feature on the PrepareJAABAData interface which I am not entirely sure what it is used for (see attached image). Would it be possible to use this "regions of interest" feature to limit a specific behavior to happen only inside a certain ROI? (e.g.: every time the mouse is inside the ROI, the assigned behavior is always "Investigating"). If not, what is this feature used for? I couldn't find any information about it on the JAABA website. [image: image] https://urldefense.com/v3/__https://user-images.githubusercontent.com/57539512/68653504-2ffc8680-052c-11ea-9676-804497daf93e.png__;!oCotSwSxbw8!XH6kb44g-qAVoZZpx0p0hfiJreJxP0CQurM9VZmrHOZoz5PVx90FADW_iHC2BDItq94$

Thank you for your time!

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[2909ft]

Thank you for the reply! Yes, I am currently using MoTR. Altough I am thinking of switching to APT at some point. "This can definitely be useful for behaviors like investigating where JAABA can potentially learn to predict investigating whenever the animal's distance is smaller than a threshold." Yes, this is exactly what I wanted to do. Does JAABA take my selected ROI into account automatically or do I need to do anything else after I am done with PrepareJAABAData? Kind regards, Filipa

[mkabra]

I'll have to check and get back to you about it. It was added a long time back and I didn't write that part.

Mayank

On Tue, Nov 19, 2019 at 2:34 PM 2909ft notifications@github.com wrote:

Thank you for the reply! Yes, I am currently using MoTR. Altough I am thinking of switching to APT at some point. "This can definitely be useful for behaviors like investigating where JAABA can potentially learn to predict investigating whenever the animal's distance is smaller than a threshold." Yes, this is exactly what I wanted to do. Does JAABA take my selected ROI into account automatically or do I need to do anything else after I am done with PrepareJAABAData? Kind regards, Filipa

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[2909ft]

Awesome, thank you so much!

[mkabra]

Hi Felipa,

I've added the option to add ROIs for MoTR. To use these, when you create a new project in JAABA, select "flies_withrois" or "mice_withrois". The difference is that in flies_withrois, it computes arena-based perframe features, so you'll have to specify the arena parameters in PrepapreJAABAData. mice_withrois doesn't compute the arena perframe features.

I couldn't test it because I don't have a MoTR mat file to work with. Can you try it out? If it fails, can you send me an example MoTR mat file so that I can debug it?

On Tue, Nov 19, 2019 at 2:44 PM Mayank Kabra kabram@janelia.hhmi.org wrote:

I'll have to check and get back to you about it. It was added a long time back and I didn't write that part.

Mayank

On Tue, Nov 19, 2019 at 2:34 PM 2909ft notifications@github.com wrote:

Thank you for the reply! Yes, I am currently using MoTR. Altough I am thinking of switching to APT at some point. "This can definitely be useful for behaviors like investigating where JAABA can potentially learn to predict investigating whenever the animal's distance is smaller than a threshold." Yes, this is exactly what I wanted to do. Does JAABA take my selected ROI into account automatically or do I need to do anything else after I am done with PrepareJAABAData? Kind regards, Filipa

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[2909ft]

Thank you so much!! Apologies for the late reply, I will be trying it out this week

Kind regards, Filipa

[2909ft]

I finally sat down on my desk and tested it :) Apologies for the delay!

Whenever JAABA is regenerating the missing files for the experiment directories, this error message pops up (see attached, it says "Error adding expdir C:\users\torrao\Desktop\JAABA-master\perframe\Exp20191204T115052: MATLAB:badsubscript: Index exceeds the number of array elements"). Is this a bug or am I doing something wrong? I will also attach a MoTR mat file so that you can try it out (on a zip file because github doesn't let me attach a mat file). Let me know if you require more information, and thank you so much once again! m1sensoryD1_tracks.zip

[mkabra]

Hi Filipa,

A file was missing in the last commit to JAABA. Can you pull and try again?

Mayank

On Wed, Dec 4, 2019 at 5:02 PM 2909ft notifications@github.com wrote:

I finally sat down on my desk and tested it :) Apologies for the delay!

Whenever JAABA is regenerating the missing files for the experiment directories, this error message pops up (see attached, it says "Error adding expdir C:\users\torrao\Desktop\JAABA-master\perframe\Exp20191204T115052: MATLAB:badsubscript: Index exceeds the number of array elements"). Is this a bug or am I doing something wrong? I will also attach a MoTR mat file so that you can try it out (on a zip file because github doesn't let me attach a mat file). Let me know if you require more information, and thank you so much once again! m1sensoryD1_tracks.zip https://urldefense.com/v3/__https://github.com/kristinbranson/JAABA/files/3921537/m1sensoryD1_tracks.zip__;!oCotSwSxbw8!VwZgcJudlL2VLLIarHMg1LY73WXFrDR12yrwK5xYYXjwIj3-BLOCfPtIIq202pyftvk$ [image: image] https://urldefense.com/v3/__https://user-images.githubusercontent.com/57539512/70138839-6e034b00-1691-11ea-9660-4647e69d4e4c.png__;!oCotSwSxbw8!VwZgcJudlL2VLLIarHMg1LY73WXFrDR12yrwK5xYYXjwIj3-BLOCfPtIIq20IQJCSRY$

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[2909ft]

I downloaded JAABA from here around 2 hours ago and that's the version I used. Did you add the missing file after that?

[mkabra]

Just about then I think :).

On Wed, Dec 4, 2019 at 5:13 PM 2909ft notifications@github.com wrote:

I downloaded JAABA from here around 2 hours ago and that's the version I used. Did you add the missing file after that?

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[2909ft]

Alright, I will try it again then :)

[2909ft]

Unfortunately it still gives me the same error message :(

[mkabra]

Sorry about that. I'll take a look.

On Wed, Dec 4, 2019 at 6:24 PM 2909ft notifications@github.com wrote:

Unfortunately it still gives me the same error message :(

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[mkabra]

Yeah, there was a bug. Fixed it. I was able to open the experiment in JAABA after that. However, note that to use ROIs, the arena type cannot be None but has to be rectangle or circle.

On Wed, Dec 4, 2019 at 6:36 PM Mayank Kabra kabram@janelia.hhmi.org wrote:

Sorry about that. I'll take a look.

On Wed, Dec 4, 2019 at 6:24 PM 2909ft notifications@github.com wrote:

Unfortunately it still gives me the same error message :(

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[2909ft]

Thank you very much! :) Now there seems to be another problem whenever I try to launch JAABA using StartJAABA. This error message appears:

StartJAABA Number of threads allocated for computation: 2 Number of threads allocated for display: 2 Error: File: JLabel.m Line: 1293 Column: 41 Invalid expression. When calling a function or indexing a variable, use parentheses. Otherwise, check for mismatched delimiters.

Error in StartJAABA (line 38) JLabel('nthreads',nthreads);

[mkabra]

My commit message got typed into the code. Sorry. Fixed that.

Mayank

On Thu, Dec 5, 2019 at 5:39 PM 2909ft notifications@github.com wrote:

Thank you very much! :) Now there seems to be another problem whenever I try to launch JAABA using StartJAABA. This error message appears:

StartJAABA Number of threads allocated for computation: 2 Number of threads allocated for display: 2 Error: File: JLabel.m Line: 1293 Column: 41 Invalid expression. When calling a function or indexing a variable, use parentheses. Otherwise, check for mismatched delimiters.

Error in StartJAABA (line 38) JLabel('nthreads',nthreads);

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[2909ft]

Thank you Mayank! It's working perfectly now :) I believe JAABAPlot might also have a bug? I get this error message whenever I try to launch it

JAABAPlot Error: File: JAABAPlot.m Line: 3709 Column: 22 Assigning to the for-loop variable 'i' is not supported in parfor-loops. For more information, see Parallel for Loops in MATLAB, "Nested for-Loops: Requirements and Limitations".

Do you know how to fix it?

[mkabra]

Seems Matlab changed the way it handles loops. I've tried to fix it. Can you test it?

Mayank

On Thu, Dec 5, 2019 at 11:20 PM 2909ft notifications@github.com wrote:

Thank you Mayank! It's working perfectly now :) I believe JAABAPlot might also have a bug? I get this error message whenever I try to launch it

JAABAPlot Error: File: JAABAPlot.m Line: 3709 Column: 22 Assigning to the for-loop variable 'i' is not supported in parfor-loops. For more information, see Parallel for Loops in MATLAB, "Nested for-Loops: Requirements and Limitations".

Do you know how to fix it?

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[2909ft]

Thank you! Yes, it fixed the bug on that line, but there's still the same one but now on line Line: 4721 Column: 23 ahahah

[mkabra]

I've tried to fix all bugs similar to these. Can you try again? If there are still issues, can you let me know what we were trying to do so that I can recreate them?

Mayank

On Fri, Dec 6, 2019 at 10:05 PM 2909ft notifications@github.com wrote:

Thank you! Yes, it fixed the bug on that line, but there's still the same one but now on line Line: 4721 Column: 23 ahahah

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[2909ft]

Seems to be working fine! Thank you very much :) Have a nice day!

[puessirvetelo]

Hi! I'm working on scoring exploratory behavior in mice towards two distinct objects. I've tracked the video with MoTR and, then, set the area surrounding each object as distinct ROIs in PrepareJAABAData. The JAABA project is set as "mice_withrois". After training and saving the JAABA project, I've exported the scores of this first video but cannot seem to find the data regarding ROIs in the scores file. Am I doing something wrong?

Thanks a lot!

Cheers, Candela

[mkabra]

Hi Candela,

The scores file stores only the predictions. The ROI details should be available in the trx file.

Mayank

On Thu, Jan 7, 2021 at 1:55 AM puessirvetelo notifications@github.com wrote:

Hi! I'm working on scoring exploratory behavior in mice towards two distinct objects. I've tracked the video with MoTR and, then, set the area surrounding each object as distinct ROIs in PrepareJAABAData. The JAABA project is set as "mice_withrois". After training and saving the JAABA project, I've exported the scores of this first video but cannot seem to find the data regarding ROIs in the scores file. Am I doing something wrong?

Thanks a lot!

Cheers, Candela

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[puessirvetelo]

Hi Mayank,

Thanks for the quick reply! Actually, I was wondering about the predictions based on ROIs, such as frames in which the behavior is being predicted within each ROI (considering I've set two ROIs in PrepareJAABAData) or distance to ROI, angle between animal's head direction, etc. Is that retrievable data? If it is, where could I find it?

Many thanks again!

Candela

[mkabra]

Hi Candela,

You can retrieve some of the data from the per-frame files which will be stored in "perframe" directory within each experiment's directory ( http://jaaba.sourceforge.net/DataFormatting.html#PerFrameDirectoryStructure). The per-frame files store the per-frame features that are computed from the input trajectories and give information about the animal's state in the current frame. The per-frame files are mat files in which the data is stored in the "data" field which is a cell array. Data in cell j stores the information about j-th trajectory/animal. The length of data{j} is the same as the length of the corresponding trajectory. The length can be short by 1 or 2 if the per-frame feature is a first derivative or a second derivative with respect to time. To find the frames that the data corresponds to look at the "firstframe" and "endframe" of the corresponding trajectory in the tracks file ( http://jaaba.sourceforge.net/DataFormatting.html#TracksFileStructure).

The per-frame files of interest are:

• dist2roi2_{j}: This gives the distance of the animal to the ROI j. There is a chance that this statistic is computed but not saved.
• mindist2roi2: This gives the distance of the animal to the closest ROI.
• dmindist2roi2: Rate of change (i.e., time derivative) of mindist2roi2. So how fast is the animal approaching or receding from the closest ROI.
• angle2closestroi2: Direction of the closest ROIs center relative to the animal's body. If the animal is facing the ROI then this will be 0, while if the animal is facing in opposite direction then it'll be pi.

There could be other per-frame files with roi2 in their names. If it's unclear what they might store based on their name, feel free to ask us.

HTH, Mayank

On Thu, Jan 7, 2021 at 9:32 PM puessirvetelo notifications@github.com wrote:

Hi Mayank,

Thanks for the quick reply! Actually, I was wondering about the predictions based on ROIs, such as frames in which the behavior is being predicted within each ROI (considering I've set two ROIs in PrepareJAABAData) or distance to ROI, angle between animal's head direction, etc. Is that retrievable data? If it is, where could I find it?

Many thanks again!

Candela

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[mkabra]

And I forgot to mention that all the per-frame features are computed from the information that is available in the tracks file. You might be better off computing the features directly from the tracks file in most cases. The only thing different for your tracks file is that it'll have an extra field "roi2" that stores the ROI information. For circular ROI with center (x,y) and radius r, roi2 will be (x,y,r,NaN) and for rectangular arena with center (x,y) and width w and height h roi2 will be (x,y,w,h).

Mayank

On Fri, Jan 8, 2021 at 6:34 PM Mayank Kabra kabram@janelia.hhmi.org wrote:

Hi Candela,

You can retrieve some of the data from the per-frame files which will be stored in "perframe" directory within each experiment's directory ( http://jaaba.sourceforge.net/DataFormatting.html#PerFrameDirectoryStructure). The per-frame files store the per-frame features that are computed from the input trajectories and give information about the animal's state in the current frame. The per-frame files are mat files in which the data is stored in the "data" field which is a cell array. Data in cell j stores the information about j-th trajectory/animal. The length of data{j} is the same as the length of the corresponding trajectory. The length can be short by 1 or 2 if the per-frame feature is a first derivative or a second derivative with respect to time. To find the frames that the data corresponds to look at the "firstframe" and "endframe" of the corresponding trajectory in the tracks file ( http://jaaba.sourceforge.net/DataFormatting.html#TracksFileStructure).

The per-frame files of interest are:

• dist2roi2_{j}: This gives the distance of the animal to the ROI j. There is a chance that this statistic is computed but not saved.
• mindist2roi2: This gives the distance of the animal to the closest ROI.
• dmindist2roi2: Rate of change (i.e., time derivative) of mindist2roi2. So how fast is the animal approaching or receding from the closest ROI.
• angle2closestroi2: Direction of the closest ROIs center relative to the animal's body. If the animal is facing the ROI then this will be 0, while if the animal is facing in opposite direction then it'll be pi.

There could be other per-frame files with roi2 in their names. If it's unclear what they might store based on their name, feel free to ask us.

HTH, Mayank

On Thu, Jan 7, 2021 at 9:32 PM puessirvetelo notifications@github.com wrote:

Hi Mayank,

Thanks for the quick reply! Actually, I was wondering about the predictions based on ROIs, such as frames in which the behavior is being predicted within each ROI (considering I've set two ROIs in PrepareJAABAData) or distance to ROI, angle between animal's head direction, etc. Is that retrievable data? If it is, where could I find it?

Many thanks again!

Candela

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[puessirvetelo]

Great! I'll look into all of that, I believe it'll be really helpful to perform this scoring.

Many thanks for all the help!

Candela