Loading edited ROI data

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  • mwoodley

    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.



    Stephane Dallongeville

    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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