Exporting ROIs to SwimmingPool

Hello,

I was wondering if there is a way to use the Spot Tracking and/or Track Manager plugins in Icy without using the Spot Detector plugin? I am trying to track spots in a movie that I have already segmented using Ilastik. Instead of using Spot Detector to detect these spots and to export an ROI to SwimmingPool, is there a way to bypass this step and to export a preexisting ROI to SwimmingPool (for example, an ROI from Label Extractor)?

Thank you!
Sally

Dear Sally,

Yes, it is possible to use the Spot Tracking and/or Track Manager plugins in Icy without the Spot Detector. You can use regions of interest (ROIs) coming from other sources than the Spot Detector in these plugins, as long as the ROIs are located in the Swimming Pool.

You could use the Connected Components plugin on the Ilastik images and tick “Swimming pool” in the Export menu to send the result to the Swimming Pool.
Connected_Components

To visualise the content of the Swimming Pool, you can use the Swimming Pool viewer plugin.
SwimmingPool

I hope this helps. Do not hesitate to upload an example of Ilastik segmentation here. It helps providing an accurate answer and it gives an example for other users having similar questions.

Best regards,
Marion

2 Likes

Hi Sally,

To complete the response from @MarionLouveaux, you can use whatever plugin generating ROI objects and use the plugin ROI to Detection to transform those ROIs to detection objects which are required by Spot Tracking plugin. You can also directly send them to the Swimming Pool (required for Spot Tracking plugin when used in interactive mode).
The plugin also exist in form of block for Protocols if you want to use that in a protocol.

Best,

– Stephane

2 Likes

Hi @Stephane and @MarionLouveaux,

Thank you both very much for your help! I was able to use Spot Tracking without Spot Detector using both of your methods.

There is one other issue I’m running into. While I am able look at the tracks from my segmented image using Track Manager, I also want to look at the area of these spots over time. However, I keep getting an error when I try to use the ROI Statistics Track Processor in Track Manager.

I have been using this protocol that I saved in order to add my segmented areas to ROI and to Swimming Pool:
Screen Shot 2021-02-16 at 12.30.57 AM

However, whenever I then use Spot Tracking (both the Simple and Advanced Interfaces) and Track Manager and then try to use the ROI Statistics Track Processor, I get an error like this (sometimes the message varies in the min/max values it lists):

I was wondering if you knew how I could resolve this issue? I’m not sure what “bounding dimension 2” is referring to and how I could change those values.

Here is a sample of an image I segmented in Ilastik that I am trying to track and measure the flares of:
0017__mC2xrGBD10_Simple Segmentation_LowerLeftQuad.tif (11.5 MB)

Thank you!

Best,
Sally

Dear Sally,

I downloaded the image sample you provided and dragged and dropped it in Icy. It opened as a Z stack, so I converted Z to T (in the Image/Sequence tab → Z/T conversion → Convert to Time). Then I ran the two blocks protocol to get the ROIs and sent them to the Swimming pool. And I opened the ROI Statistics Track Processor to display a plot with the Area. I didn’t encounter any error message.

Are you going through the same steps? Do you encounter the error all the time or only from time to time (on some images only for instance)?

Best regards,
Marion

1 Like

Hi Marion,

I do go through those same steps when I encounter the error. However, the error does not appear all the time. Sometimes I am able to get the ROI Statistics Track Processor to work, but when I do encounter the error message, it seems as though it appears for all the images I try rather than just occurring for a certain few images. I think the message may correspond to certain images which then affect the ROI Statistics Track Processor for all following images, even if they normally seem to work with the processor.

Here’s one image that seems to initiate the error message:
0002__mC2xrGBD16_Example.tif (10.9 MB)

Thank you!
Sally

Dear Sally,

I managed to reproduce your error with the second image you sent :+1:
I will investigate the issue further and come back to you soon.

Best regards,
Marion

1 Like

Dear Sally,

We identified the problem and fixed it but you will need to wait a bit to get the new version of ROI Statistics plugin. It requires the new version of Icy to work properly (we made some changes for better homogeneity between the plugin and the ROI table from the application).
Thanks for your patience !

Best,

– Stephane

1 Like