Link spot detection to segmented masks over time

[Andrew Seeber]

Hi,

I've been using Icy and I like it a lot. The protocol blocks make things really easy. I'm trying to troubleshoot a protocol and would love some external help to get closer to a final working version. I have attached the protocol and a test image. 

The aim of the protocol is get the number of spots in a nucleus over time. I use active contours to create ROIs that are then fed into the spot detector block. That part works okay. The part that is missing is to link the ROIs from active contours to the detected spots to get the number of spots / cell nucleus. How would I do this? I could process each frame of the time series individually, but then I lose the information color coding the ROIs  through time that active contours does so well.

Thank you for any help in advance,

Andy

[Alexandre Dufour]

Hi Andrew,

Glad Icy fits your needs, we put a lot of effort into it.

For this very purpose I’d suggest you add the “ROI inclusion analysis” block, which should do what you ask.

Alexandre

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<Cell for spot detection.tif><Cell for spot detection.xml><Spot detection in time.protocol><Spot detection in time.protocol_screenshot.png>

[Andrew Seeber]

Dear Alexandre,

Thanks a lot, the "ROI inclusion analysis" does exactly as advertised. I've attached the final protocol here in case anyone else requires something similar.

Thanks again. Icy is really great and I'm glad that there is a community making it stronger.

Best wishes,

Andrew

On Thu, Aug 31, 2017 at 9:14 AM, Alexandre Dufour <adu...@pasteur.fr> wrote:

Hi Andrew,

Glad Icy fits your needs, we put a lot of effort into it.

For this very purpose I’d suggest you add the “ROI inclusion analysis” block, which should do what you ask.

Alexandre

On 31 Aug 2017, at 08:23, Andrew Seeber <andy....@gmail.com> wrote:

Hi,

I've been using Icy and I like it a lot. The protocol blocks make things really easy. I'm trying to troubleshoot a protocol and would love some external help to get closer to a final working version. I have attached the protocol and a test image. 

The aim of the protocol is get the number of spots in a nucleus over time. I use active contours to create ROIs that are then fed into the spot detector block. That part works okay. The part that is missing is to link the ROIs from active contours to the detected spots to get the number of spots / cell nucleus. How would I do this? I could process each frame of the time series individually, but then I lose the information color coding the ROIs  through time that active contours does so well.

Thank you for any help in advance,

Andy

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<Cell for spot detection.tif><Cell for spot detection.xml><Spot detection in time.protocol><Spot detection in time.protocol_screenshot.png>

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