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Hi,
After running the separation of touching objects on selected vignettes and reprocessing the images to include the separation mask, Zooprocess seems to create duplicates of the last 3-5 images in the work folder. I wonder what is the reason for the duplicates and if this is a common occurrence. I noticed something weird was going on when the measurement file meas.txt had less rows than there were images. It seems that the duplicates aren't included in the measurement information which is good.
My second question has to do with the measurement file. The label column has the name of the sample on every row instead of the label of the corresponding image. There doesn't seem to be a very good way of matching a measurement to the correct image when the label doesn't work as an id. Should I use the row number as a way to connect measurement to an image or am I missing something else?
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Hi,
Answers hereunder:.
After running the separation of touching objects on selected vignettes and reprocessing the images to include the separation mask, Zooprocess seems to create duplicates of the last 3-5 images in the work folder. I wonder what is the reason for the duplicates and if this is a common occurrence.
►If you do not want to see the duplicates at this step of the process, you need to delete the vignettes before re-processing the sample in order to not have twice the same vignettes displayed. In any case, the vignettes names are different and thus it is normal to have duplicates. If the separated obtained object is too small, it won't be recorded because of size threshold in the config file.
Nevertheless, the final export folder for Ecotaxa will take care of everything for you.
I noticed something weird was going on when the measurement file meas.txt had less rows than there were images
►Correct, the file data is the one created before the separation and does not include the created vignettes from separation.
My second question has to do with the measurement file. The label column has the name of the sample on every row instead of the label of the corresponding image. There doesn't seem to be a very good way of matching a measurement to the correct image when the label doesn't work as an id. Should I use the row number as a way to connect measurement to an image or am I missing something else?
►This file is not used actually, it is for production only...
The only features used is the Data section of the PID file.
But again do not care about these, the only important file is the ECOTAXA.tsv file
SF
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Great, thank you for your reply! So after running the separation of the touching objects, the ecotaxa.tsv file is automatically updated with the correct measurements? Did I understand this correctly?
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Hi,
Yes, it is correct.
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If the ecotaxa .tsv file with the measurement info is updated automatically after running the separation of the touching objects, then how is it possible that the file has less rows than there are images in the folder? Surely every image should be measured? EDIT: This seems to be a problem with one specific project. Any ideas why?
If the separated obtained object is too small, it won't be recorded because of size threshold in the config file.
What is the size threshold and can it be changed?
Last edited by kaskelotti (2023-03-21 12:15:36)
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Hi,
You can modify the size threshold with Zooprocess.
To do so, open "edit configuration file"
Then change value "ESD min for organisms to be analyzed" which is by default set at 0.300 mm.
SF
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Hi,
Thank you! At the settings is says that the value should be 0.300. Can I ask why that has been chosen as the default? What are the downsides of lowering the value?
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Hi,
This is a limit for the reconnaissance. You won't get much below 300µm as the resolution of the hardware is limited at 280µm.
The process will take more time.
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