User: Bernd Fischer

gravatar for Bernd Fischer
Bernd Fischer540
Reputation:
540
Status:
Trusted
Location:
Germany / Heidelberg / DKFZ
Website:
http://www.dkfz.de/en/...
Scholar ID:
Google Scholar Page
Last seen:
1 year, 10 months ago
Joined:
6 years, 4 months ago
Email:
b********@dkfz.de

Posts by Bernd Fischer

<prev • 52 results • page 1 of 6 • next >
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Answer: A: compute Haralick features
... In a nutshell, Haralick features compute the correlation of intensities of neighboring pixels. In this way you compute, if a certain pattern is repeated or not. However, there exists textures with difference scale. Some textures are repeated every two pixels others are repeated every 10 pixels. With ...
written 23 months ago by Bernd Fischer540
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Job: PhD Positions in Computational Cancer Research
... Are you interested in solving fascinating biological or medical questions computationally? At the German Cancer Research Center (DKFZ) in Heidelberg, Germany’s largest biomedical research institute, computational scientists work at the forefront of cancer research. They combine inter­disciplinary ...
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Answer: A: phyloseq biom json format conversion needed to hdf5 format for qiime
... biom is a CRAN package, you should directly write to the respective CRAN mailing list or to the authors of the package. There exists as well a vignette for the biom package: https://cran.r-project.org/web/packages/biom/vignettes/biom-demo.html    ...
written 2.0 years ago by Bernd Fischer540
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Answer: A: Focal stacking of images in R/EBImage
... The easiest way to combine images from a confocal microscope is a max-projection, which can be obtained by Img = readImage(c("img1.tif","img2.tif","img3.tif","img4.tif")) MaxProj = apply(Img, 1:2, max) display(MaxProj) In many cases this is sufficient. However, other algorithms are not availabl ...
written 2.1 years ago by Bernd Fischer540
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Comment: C: hdf5load equivalent for RHDF5
... You can use H5close() or H5Fclose(h5file) to close the file in between. Check h5listIdentifier() for a list of all open HDF5 handles. Close them, once you don't need them anymore. ...
written 2.5 years ago by Bernd Fischer540
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Job: PhD Positions in Computational Cancer Research
... The German Cancer Research Center (DKFZ) in Heidelberg, Germany’s largest biomedical research institute, is searching for PhD students in computational sciences (computational biology, bioinformatics, imaging, biostatistics, and related topics). The PhD program provides funding for PhD students. The ...
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Answer: A: hdf5load equivalent for RHDF5
... I updated the rhdf5 package. From version 2.15.5 on, one can now use the $-operator to read data: h5file = H5Fopen("file.h5") h5file$A h5f$'A' The &-operator to get a reference to a HDF5 group or dataset and list the content of a group h5f h5f&'A' h5f&'/g1/g2/A' h5d = h5f&'A' h ...
written 2.6 years ago by Bernd Fischer540
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Answer: A: hdf5load equivalent for RHDF5
... The functionality seems to be useful. I will try to add such these functions to rhdf5 as well. This requires a little bit more work to catch errors etc..   ...
written 2.7 years ago by Bernd Fischer540
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Answer: A: hdf5load equivalent for RHDF5
... You can define the following functions that simulate the behavior: library(rhdf5) hdf5load <- function(filename) { h5file <- H5Fopen(filename) h5file } `$.H5IdComponent` <- function(h5id, name) { variable = h5read(h5id, name) } The following code shows an example how to use it. ...
written 2.7 years ago by Bernd Fischer540
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Answer: A: rhdf5 H5Dget_create_plist implementation
... H5Dget_create_plist is implemented in rhdf5 2.15.1 (available tomorrow evening).  With  library(rhdf5) f = H5Fopen(f, "myfile.h5") d = H5Dopen(f, "A") p = H5Dget_create_plist(d) H5Pget_chunk(p) you can access the chunk size of dataset A in the HDF5 file "myfile.h5". ...
written 2.9 years ago by Bernd Fischer540

Latest awards to Bernd Fischer

Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: voom for spectral counts
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Manage H5Pset_layout in R
Scholar 2.6 years ago, created an answer that has been accepted. For A: hdf5load equivalent for RHDF5
Scholar 2.6 years ago, created an answer that has been accepted. For A: Suppressing rhdf5 error messages
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Manage H5Pset_layout in R
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: voom for spectral counts
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Manage H5Pset_layout in R
Scholar 4.1 years ago, created an answer that has been accepted. For A: Manage H5Pset_layout in R

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