ROI statistics – workbook to file size limit in text format?

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    I am having issues exporting the spot stats from my spot detector as it seems I am getting to the size limit of both workbook and text export…
    I have 98529 spots detected (over 193 frames on several nuclei per frame – already taking only spots >4 size)… picture in the next post

    any solution to bypass this? the protocol goes through all the analysis but then does not write the data to the file which is a bit sad and I can’t use the rest of the analysis.

    I’d rather not crop if I can avoid it (because of issues later on finding the ringht cells etc).
    but is this something solvable?



    files where spot stats could not get exported are 1kb

    Stephane Dallongeville

    Hi Debbi,

    XLSX should be able to handle more than 1 000 000 rows while XLS is limited to 65536 rows maximum.
    ROI Statistics export in XLSX format by default, so i don’t understand why it doesn’t work in your case.

    Does the problem appears with the ROI Statistics and ROI inclusion analysis plugin or only with the latter ?
    In the meantime I will try to replicate the issue.


    – Stephane

    Stephane Dallongeville

    We updated both ROI Statistics and Workbook plugin which may fix some weird issues when number of ROI is > 65535 (wasn’t directly due to the size of XLSX file but more to the processing queue size). We also fixed a performance issue during workbook generation when ‘Color’ field was exported. Can you tell us if that fixed your problem ? Thanks.

    – Stephane


    it again did not work… I get emtpy excel xlsx files – below the screenshot of the last image… snif

    one idea… could the available RAM limit the writing? ie I guess the intermediate results are stored somewhere, if there is not enough RAM dedicated to the storing for big images, could that play a role?

    I currenlty have 34.2Gb of RAM for icy and it does not seem to be using cache memory or disk…

    just a thought

    I did another trial overnight (still running) with 3 images (193 time points, 900mB) and an output in TXT and it seems to have worked for the first time ever…

    though if I try and touch the program it will freeze

    However, it took a looong time and I have no clue why the 2nd image took so long

    Active contour: 1h20 (5521 ROI)
    spot detector: 8 min (199247 detected scale 1 90%, 109151 filtered >4px)
    ROI inclusion analysis: 1h42 min

    image 2:
    active contour 8h49min (5617 ROI – 5061 filtered)
    spot detector 10 min (189 961 ROI detected scale 1 90%, 98529 filtered >4px)
    ROI inclusion analysis: 58 min

    image 3 is still running active contour….

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