User: Mathieu Gendarme

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8 months ago
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Posts by Mathieu Gendarme

<prev • 19 results • page 1 of 2 • next >
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Comment: C: EBImage computeFeatures error
... Dear all, I have made some progress in understanding where the issue is coming from. When I compute individually computeFeatures.basic; computeFeatures.moment; computeFeatures.shape; they return the same amount of rows, however computeFeatures.haralick retrieves a higher amount of rows indicating t ...
written 6 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... Thank you very much Andrzej! You pointed out that the data might not be the right one and you are correct, with the data of my first archive file I do not get an error. Here is the proper data set leading to a failure at position "00005": https://www.dropbox.com/s/uog8u6upvlwblxd/IF015_plate002_p ...
written 7 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... OK that works as well. Please find the two objects here: https://www.dropbox.com/s/v6y8o0z5vqaj3k8/Donut.RData?dl=0 https://www.dropbox.com/s/nu0888x0nwtti18/Img488.RData?dl=0 Cheers ...
written 8 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... The output of ImageProcessing(Image = AllImages, Plate = 2, Well = "A5", Position = "00005") with options(error=recover) doesn't change to much. > ImageProcessing(Image = AllImages, Plate = 2, Well = "A5", Position = "00005") Error in (function (..., deparse.level = 1) : number of rows of ...
written 8 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... Hi Andrzej, I would love to provide the Donut mask and the Img488 outputs. However I have a problem with the Donut, when I want to writeImage it rescales the labels and transforms everything above 0 to 1s. If I do normalize than I get individual values for each mask but not integers which I assume ...
written 8 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... Thanks Andrzej for trying it out, Here is what get from the traceback: [1] "Plate: 2; Well: A5; Position: 00001; Time:2018-11-21 12:32:21" [1] "Plate: 2; Well: A5; Position: 00002; Time:2018-11-21 12:32:41" [1] "Plate: 2; Well: A5; Position: 00003; Time:2018-11-21 12:32:56" [1] "Plate: 2; Well: A ...
written 8 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... Just to mention I did try to run this as well on a linux machine with ubuntu 18.04 and get the exact same message... Very strange that it doesn't happen to you Mike. Something must be wrong at my side. ...
written 9 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... I also did try your script Mike and I get the exact same issue. I really don't know anymore how to tackle this problem. ...
written 9 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... Thanks for the advice. I did manage to do it and to be on the safe side I even re-installed fresh R and RStudio with all libraries (which did work once I got the admin rights). I then tried to re-run the script I sent and got the same error after Position 00004 [1] "Plate: 2; Well: A5; Position: ...
written 9 weeks ago by Mathieu Gendarme10
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Comment: C: EBImage computeFeatures error
... Thanks a lot for your help. It seems that I have a bigger problem as downgrading is an issue. I tried this (before installing EBImage from a ealier version): > BiocManager::install(version = "3.7") # latest 3.8 Getting this error: Bioconductor version 3.7 (BiocManager 1.30.4), R 3.5.1 (201 ...
written 9 weeks ago by Mathieu Gendarme10

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