Active contours plugin issue

[Aurélie Martinez]

Hi everybody,

I'm currently discovering this software and I'm really impressed by all we can easily do with it! 

I would like to know if other people had some problem with the option "Send to track manager" when we want to track objects over time? 

Indeed, tracks were no longer sent to the track manager and I'm not able to see them anywhere.

Has this problem been reported lately?

Thank you,

Aurélie

[Alexandre Dufour]

Hi Aurélie,

Thx for the nice comment, we do try our best to make arguably-complex algorithms look simple to the user.

I’ve tried this morning and the export seems to work fine. From your email I understand that the export was working in the past, is this correct? If so, when did it stop working?
Also, is it possible that some new plugins were installed (or updated) while the "active contours" window was open? This could be one issue, but is short-lived since re-opening the active contours plugin fixes the issue.
Otherwise, perhaps a small test case would help us investigate further.

Cheers
Alexandre

[Aurélie Martinez]

Hi Alexandre,

Thank you for your quick answer! 

In fact, I played a little more with this plugin and I just figured something:

You right it's working when you put "Export ROI_NO" but not anymore with the other three option (ON_INPUT ; ON_NEW_IMAGE ; AS_LABEL).

I would like to have access to the tracks of my cell population and the mean intensity per nucleus and per frame in the same time.

For that, I started with HK-Means and one first Active Contour just on my first frame to set all the settings. 

After, I wanted to launch the tracking during time with Active Contours again.

Like ROIs from HK-Means are already on the ROIs window,I would like choose the option "ON_NEW_IMAGE" to keep just the ROIs/frame obtain with Active contours and at the same time to have access to my tracks in Track Manager. 

I don't know if this problem can be solved. If not, I always can launch one first tracking with Active Contours with "Export ROI_NO" to have access to the track and restart an another one with "ON_NEW_IMAGE" to have my mean Intensities measured in each ROIs. It will be just twice as long.

I hope my explanations are clear, thank you again for your answer,

Aurélie

PS: the plugin is updated and sorry for the misunderstanding, it never worked for me (at least with a different option than Export ROI_NO).

[Alexandre Dufour]

Hi Aurélie,

> On 14 Sep 2017, at 18:12, Aurélie Martinez <martinez....@gmail.com> wrote:
>
> In fact, I played a little more with this plugin and I just figured something:
> You right it's working when you put "Export ROI_NO" but not anymore with the other three option (ON_INPUT ; ON_NEW_IMAGE ; AS_LABEL).

Correct. This is meant to happen in protocols, but not in the standalone interface. I have just pushed an update to fix it. Thx for the report!

> I would like to have access to the tracks of my cell population and the mean intensity per nucleus and per frame in the same time.
> For that, I started with HK-Means and one first Active Contour just on my first frame to set all the settings.
> After, I wanted to launch the tracking during time with Active Contours again.
> Like ROIs from HK-Means are already on the ROIs window,I would like choose the option "ON_NEW_IMAGE" to keep just the ROIs/frame obtain with Active contours and at the same time to have access to my tracks in Track Manager.

Although this works (especially after my fix), you have an even faster option, since ROI descriptors are available straight from the track manager. Basically once you have exported your tracks, you can add a track processor called “ROIStatisticsTrackProcessor” that lets you measure (and plot!) the various descriptors for each tracked object. All this with spreadsheet export.

Let me know if that fits your need (and simplifies your life somehow…)

Cheers
Alexandre

[Aurélie Martinez]

Hi Alexandre, 

Thank you so much, your answer and your fixing are all what I needed! I tried this morning and it's working!

Aurélie