Measuring intensities from tracked cells

KNIME Extensions Image Processing
#1

Hello,

 I am trying to track cells and measure the Fret ratio of a biosensor over time and then plot the individual cells on a line plot. I was hoping to use Knime so I could easily track back a given line on the plot to a cell in the original movie using the interactive segmentaion and hiliting abilities of Knime and Knime Image Processing.

 I am able to track my cells using the Trackmate node, the problem I encounter is how to extract the mean intensities per timepoint from these tracked cells? When I use the Image Segment Features with the tracked cells I apparently can only get the mean intensity over the whole time for each cell. Then I thought I split time before proccessing but Trackmate needs a volume to work. Splitting after using trackmate is not straight forward as there is no labeling splitter (or did I miss it). Is there any easy way to do that? Did I miss a specific node?

I hope this is more or less clear, in other words I could ask how to do line plots over time from the tracks generated in the trackmate example? I hope you can help me because being able to track back the cells using the image segmentation/hiliting capabilities would be great!

Thanks

Cheers

Yannick

#2

Hello Yannick,

 

you could use Slice Loop Start -> Image Segment Feature -> Loop End (not Slice Loop End) after the tracking with Trackmate. That way you would get the mean intensity for each track for each "slice" and you could use the "Iteration" column to identify the timepoint.

 

I hope this helps.

#3

Hi,

Thanks that worked, I then pivoted the table and was able to plot the tracks with the line plot node. Now my ultimate goal would be to hilite a line (track) and see the corresponding cell using interactive segmentation view. Is that even possible? It doesn't seem to be possible to select lines in the line plot node, only a given timepoint, is that true?

Do you know wether there is a way to do that anyway?

Thanks again

Cheers

Yannick

#4

Hi Yannick,

I attached an example workflow that will work with the latest KNIP nightly build. I found a way to avoid the Slice loop so it should run a lot faster.

I hope that helps you out.

Greetings,

Gabriel

#5

Hi Yannick,

We have developed a Node to provide a mapping from data points to the Tracks. It is the Track Hilite Propagator Node which you can find in the KNIP nightly builds.

Greetings.

Gabriel