"simple" tracking task

Hi fellows, first of all thanks so much for your contribution with this great software!

In my case, I use CP to obtain the trajectories of moving objects and then get their speed (attached pipeline). The input data for CP is a stack of 1200 TIFF images.

The quotation marks in the title of the post mean that I don’t intend to say that tracking is simple, actually I am aware that it is a really complex matter. But this is a very basic, simple use of the tracking module.

I have two questions:

  • Most important is about how long it takes for this “simple” tracking use. Is it OK that it takes several hours (at least 3.5, when I hide the windows of all modules). Or maybe I am doing something wrong or redundant? Maybe this is normal for the number of files. I run it on a Toshiba Tecra, Centrino Duo, WinXP, 2GHz, 3GB of RAM.

  • Less important but related: I use ImageJ for thresholding the image sequence, therefore the input images are already binary. Is there a way to directly skip the thresholding step in IdentifyPrimaryObjects module? I tried to tell CP that it was a Binary Image (by selecting “Binary Image” in the “Thresholding method” field) but CP tells me that it did not find a binarized image… but most likely I am doing/thinking wrongly in this. I want to feed CP with a binarized image and would like to simply skip the thresholding by CP (this is not only to save time, it is that by now I am more comfortable by adjusting the threshold with ImageJ).

Again, thanks so much for CellProfiler!!!

Update: by looking into the DefaultOUT_Image.csv file (GREAT idea by the way, especially for finding actual or potential errors!!) I can see that the most time-consuming module is the tracking one (approx. 10 seconds per image). So I realize now that the threshold does probably not a big difference (as it belongs to the Identify module).
S5_track.cp (6.33 KB)

Sorry for the delay on this question!

[quote=“rodrigo”]

  • Most important is about how long it takes for this “simple” tracking use. Is it OK that it takes several hours (at least 3.5, when I hide the windows of all modules). Or maybe I am doing something wrong or redundant? Maybe this is normal for the number of files. I run it on a Toshiba Tecra, Centrino Duo, WinXP, 2GHz, 3GB of RAM.[/quote]

Depending on the complexity of the identification and/or tracking, this may in fact be perfectly normal.

You might want to apply ColorToGray (in case that it’s a color image that appears to be binary) or ApplyThreshold with a threshold of 0.5. Also, if you can get ImageJ to output a label matrix rather than a binary image (perhaps by using the “Analyze Particles” plugin), you can use LoadImages to load the matrix as objects immediately rather than an image to process, by selecting “Objects” from the “Load the input as images or objects?” setting. This would allow you to bypass using IdentifyPrimaryObjects entirely.

Regards,
-Mark