User: Andrzej Oleś

gravatar for Andrzej Oleś
Andrzej Oleś470
Reputation:
470
Status:
Trusted
Location:
EMBL Heidelberg, Germany
Website:
https://github.com/aoles
Twitter:
andrzejkoles
Scholar ID:
Google Scholar Page
Last seen:
1 week, 3 days ago
Joined:
4 years, 8 months ago
Email:
a***********@embl.de

Posts by Andrzej Oleś

<prev • 63 results • page 1 of 7 • next >
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Answer: A: EBImage cannot read .png images from Image.R
... Your description indicates a problem with either the input filename or downstream package functions calling EBImage functions. The quotation mark in the error message looks suspicious indeed, as it suggests that the filename passed to readImage wrongly contains a quotation mark, i.e. filename.png". ...
written 10 days ago by Andrzej Oleś470
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Answer: A: Issue with pandoc-citeproc when rendering the f1000 article Rmd file from BiocWo
... Hi Leo, there seems to be a problem with version compatibility between pandoc and pandoc-citeproc as described in the issue you linked. Apparently your pandoc-citeproc version is outdated, as on my linux machine I have a much more recent version of pandoc-citeproc 0.10.1 vs. yours 0.5 even though I ...
written 11 days ago by Andrzej Oleś470
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Comment: C: Error during EBImage installation
... For the record, Martin's solution applies to Debian based Linux distributions such as Ubuntu. On Red Hat Linux (e.g. Fedora) the system dependency can be obtained by yum install fftw-devel.   ...
written 28 days ago by Andrzej Oleś470
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Answer: A: Error during EBImage installation
... Dear Maarten, the output of your sessionInfo indicates that you are running R under OS X Sierra, but attempt to install packages from sources. Is there any particular reason why you don't use mac binaries? Platform-specific binary packages typically include the necessary dependencies, so you should ...
written 28 days ago by Andrzej Oleś470
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Comment: C: Focal stacking of images in R/EBImage
... Hi Phil, this method is now provided by the new Bioconductor package MaxContrastProjection. The package also implements the novel maximum contrast projection algorithm which avoids some of the problems of the former method and yields cleaner results. ...
written 8 weeks ago by Andrzej Oleś470
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Answer: A: get pixel coordinates interactively with EBimage
... It's possible to retrieve pixel coordinates interactively by using the function locator() in combination with the "raster" mode of display, as in the following example. library("EBImage") # load and display a sample image img <- readImage(system.file("images", "sample.png", package="EBImage")) ...
written 8 weeks ago by Andrzej Oleś470
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Answer: A: Deals with image value superior to 0,1 range
... Dear Valérian, you can save your images as 16 bit TIFFs and transform between the integer and double pixel representation on read/write. For this when saving your images you would divide the pixel values by the maximum value which can be stored as unsigned integer (UINT16), which is 2^16-1.  To tra ...
written 9 weeks ago by Andrzej Oleś470
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Comment: C: EBImage / problem in running the code via Rscript
... Thanks Martin, I basically came to similar conclusions. I was wondering what would be the best way of fixing this on our side. The problem seems to be related to the fact that methods package needs to be attached in order to manipulate S4 objects by abind, as running the following in Rscript also f ...
written 3 months ago by Andrzej Oleś470
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Comment: C: Workflow highthroughputassays can't install properly
... I assume you previously had a working installation of rgl, but probably because of some system changes (?) it stopped loading. The easiest thing to try is to re-install the package. install.packages(rgl)   ...
written 4 months ago by Andrzej Oleś470
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Answer: A: Workflow highthroughputassays can't install properly
... The error message indicates some problems with the rgl package, so please double check that you meet the required system dependencies. Also, please note that the fact that the workflow package is not provided as a mac binary in first place indicates that its author for some reason decided not to su ...
written 4 months ago by Andrzej Oleś470

Latest awards to Andrzej Oleś

Scholar 10 days ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 14 months ago, created an answer that has been accepted. For A: reactive CellCODE heatmap
Scholar 14 months ago, created an answer that has been accepted. For A: Not able to display actual grayscale image using EBImage
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 14 months ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Scholar 14 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 14 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 19 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 23 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop

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