User: Andrzej Oleś

gravatar for Andrzej Oleś
Andrzej Oleś430
Reputation:
430
Status:
Trusted
Location:
EMBL Heidelberg, Germany
Website:
https://github.com/aoles
Twitter:
andrzejkoles
Scholar ID:
Google Scholar Page
Last seen:
3 days, 22 hours ago
Joined:
4 years, 7 months ago
Email:
a***********@embl.de

Posts by Andrzej Oleś

<prev • 59 results • page 1 of 6 • next >
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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 25 days ago by Andrzej Oleś430
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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 26 days ago by Andrzej Oleś430
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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 29 days ago by Andrzej Oleś430
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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 8 weeks ago by Andrzej Oleś430
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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 3 months ago by Andrzej Oleś430
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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 3 months ago by Andrzej Oleś430
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Answer: A: Error occurred, creating Vignette in LateX style 2.0
... To address the problem of file paths containing spaces I've added an option in BiocStyle v2.3.28  to copy the supporting files to the vignette directory and refer to them by relative paths. To enable it, use BiocStyle::latex2(relative.path = TRUE)     ...
written 5 months ago by Andrzej Oleś430
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... Please note that this solution is not portable and will only work on machines which have the directory containing Bioconductor2.sty added to the LaTeX PATH. In particular, your vignette will fail to compile on Bioconductor builders once you submit the package for review. See my answer below for a m ...
written 5 months ago by Andrzej Oleś430
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... Thanks Mattia! Can you please check whether substituting the line loading Bioconductor.sty by any of the following two lines circumvents the problem? \RequirePackage{"C:\Program Files\R\R-3.3.2\library\BiocStyle\resources\tex\Bioconductor"} \RequirePackage{{C:\Program Files\R\R-3.3.2\library\Bio ...
written 5 months ago by Andrzej Oleś430
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... Good call Martin! Mattia, can you maybe show us the header of the intermediate .tex file containing the relevant call to Bioconductor*.sty? ...
written 5 months ago by Andrzej Oleś430

Latest awards to Andrzej Oleś

Scholar 13 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 13 months ago, created an answer that has been accepted. For A: reactive CellCODE heatmap
Scholar 13 months ago, created an answer that has been accepted. For A: Not able to display actual grayscale image using EBImage
Scholar 13 months ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 13 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 18 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 22 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop

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