Live-cell imaging


#1

Dear Team,
Recently, I found CellTracker which can perform live-cell imaging and all.
However, I’m a user of CP and I found CP’s features as very informative and valuable. So, is there a way to perform the live-cell imaging using CP.
Or, is there a way to connect CellTracker and CellProfiler where I can use majority of CP pipeline (that I made earlier) and still can include CellTracker somehow.
Thanks in advance for the support.
Mridul KK


#2

Hi,

For tracking objects in CellProfiler, there is a module (TrackObjects) that is still beta version but has been released with 5811. As far as using CellTracker within CellProfiler, I think the easiest thing right now would be to save your CP-created images and feed them to CellTracker. But, both CP and CellTracker are written in Matlab, so if the source code of CellTracker were available I think interfacing them (ie making a CellTracker “module”) would be doable. Right now I don’t believe we have plans to interface with the CellTracker project, but you could definitely contact them yourself about getting the source code to make your own module.

~kate


#3

Hi Kate,
I’m using the following pipeline in CP for cytoplasm-nucleus translocation assay.

Pipeline:
LoadImages
LoadSingleImage
LoadText
CorrectIllumination_Apply
CorrectIllumination_Apply
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifySecondary
IdentifySecondary
IdentifyTertiarySubregion
IdentifyTertiarySubregion
MeasureCorrelation
MeasureObjectIntensity
MeasureObjectIntensity
MeasureObjectAreaShape
MeasureTexture
MeasureTexture
CalculateRatios
CalculateRatios
ClassifyObjects
ClassifyObjects
ClassifyObjects
CalculateStatistics

Primarily interested for intensity measurements for single cells (which I can get from CP). But for tracking them individually, I want to use CellTracker. As you said, “easiest thing right now would be to save your CP-created images and feed them to CellTracker”…
I want to know that in the CP pipeline, where I can incorporate the celltracker functionality.
Also, for each image taken in CP for illumination correction, how can I save the resultant image for each of input image taken.
Thanks
Mridul KK


#4

Hi,

For a full answer to you question as to how to interface CP and CellTracker, you would probably need to contact them, as Kate mentioned, and find out what format the images need to be in order to be used as input into their program. Since have not yet done any work with CellTracker, we cannot answer this question ourselves, but they should be able to.

That said, most likely, it is likely to assume that they take their images as some sort of image sequence or movie format. Therefore, if you save the images after each cycle, you can produce image files that might be usable by CellTracker. You can use the SaveImages module to do this, which can create either movies or sequential image files.

Similarly, you can use SaveImages to save your resultant images after illumination correction. Have a look at the documentation for the full details.

Hope this gets you started,
-Mark


#5

Thanks Mark,
I’m already in process to make a interface CP and CellTracker. Hope, I should be able to fix it soon.
Will post you, on my success.

Mridul KK


#6

Interesting! let us know how that interface goes.

Another question for you: did you try the TrackObjects module in CellProfiler, and did it fail to meet your needs for some reason? We are in the process of considering how to improve it, so knowing this would help us to plan.
Anne