Efficient method for creating separation mask?

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Efficient method for creating separation mask?

Post  msutor on Wed Aug 19, 2009 7:03 pm

We are exploring the different methods of creating a separation mask. We have a large set of samples (over 5000) that require some separations to be specified after the scan (for example, a number of the samples contain hydroids and other sticky things that make separation of organisms without a large amount of damage impossible). We have explored processing the converted image and checking the option to create the separation mask and we have explored the separation using vignettes function. While both methods work, we are finding that they are potentially very time consuming. For example, we have found that if we use the separation using vignettes function, if we wish to save our work and return to the image to continue processing the next day, we have to page through all of the vignettes that we have already corrected (made any necessary cuts to) and with approximately 1000 vignettes per image, this is time consuming. Likewise, we have found that if we process the converted image with the selection to create the separation mask, if we choose to stop the process and save the results, we cannot return to the same image and continue the analysis and it is a little worrisome to leave work unsaved to avoid this issue. We are seeking any advice that experienced users may have. It is entirely likely that we are not aware of some features of the Zooprocess software or that we are simply faced with some messy samples that require more work. I should note that these samples are from a historically important time series and we are exploring if we can create a digital archive of the entire sample. While the sample volume is not terribly large, due to some of the smaller organisms present we are splitting to 1:32 and it is not really feasible to split any further. We have also explored size fractionation but that had some issues as well and is not a good option for these samples. Any advice would be welcome as we decide how to proceed!

Malinda Sutor

msutor

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Separation methods and strategies

Post  picheral on Fri Aug 28, 2009 10:31 am

Dear Malinda,
I agree that this separation is very time consuming. As you mentionned, it is also necessary to separate some samples anyhow... and it is a problem to do it partially. As far as I know, there are very few users who use these tools. We are not !
I have ideas for a faster tool working on the global "msk" image but I do not have any time to write any new tool for the moment and probably for the next months !
Regards
Marc P.

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