Loading edited ROI data

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    mwoodley May 2, 2019 at 1:07 am

    I am using ICY in order to detect beta cell insulin granules in electron micrograph images and unfortunately have run into a problem. My method relies on using ICY spot detection to detect insulin granules, which works quite well, however there is always a decent amount of false detection I hope to remove.

    To do this I have exported to ROI data into an excel table where I filter it based on several factors, intensity, size, sphericity, etc. My issue is I am now wanting to import the edited ROI back into excel to see how my changes have affected the detections.

    I have converted the excel/csv data back into XML format and the files appear to be formatted identically, but the edited data set contains fewer ROIs as it has been filtered. No matter when I do I cannot seem to import these ROIs back into ICY, either the process does not work at all or sometimes I will get an error ‘java.lang.NumberFormatException: For input string “78”‘.

    Does anyone know what could be my issue here, or if there is a better way to complete this process?

    any help would be appreciated.

    Cheers,

    Marcus

    Stephane Dallongeville May 3, 2019 at 4:04 pm

    Hi Marcus,

    I’m not sure to understand your complete workflow, it looks like you’re trying to filter your data in excel and then get them back in Icy ? why don’t you try to directly filter those ROIs (rom Spot Detector) in Icy ? You can use the ROI table to add properties and sort on them (so you can easily remove ROIs under a specific value for the sorted column). You can also do that really quickly using the Protocols in Icy (with the ‘filter ROI’ block).

    – Stephane

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