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Christoph Moehl

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13 Sep 2013 Screenshot imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl data import, biotech, zvi, lsm, avi, bmp 50 11
  • 4.5
4.5 | 7 ratings
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28 Jun 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl

I suggest to use the matlab function from openmicroscopy (see Curtis Ruedens post).

When I published imreadBF here, the original importer bfopen had some drawbacks. But this seems to be solved now.

02 Apr 2012 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl

dear zhao and jian jiang

here is a way to read out the java hashtable as strings:

datname='good.oib'
meta=imreadBFmeta(datname);

parameterNames=meta.raw.keySet.toArray
values=meta.raw.values.toArray

This gives you all the rawdata. However, the parameternames are somewhat cryptic and you have to find out what is the important parameter for you.

15 Mar 2012 Robust Data File Reading utility (RDFREAD) Imports data from a comma- or tab-delimitted file. Author: Michael Boldin

great tool.

i just added

fclose(fid)

at the very end of the function. Otherwise it gave an error when calling repeatedly the function ("too many files open")

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02 Jun 2014 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl Ignacio

Hi,

I've been trying to use the imreadBFmeta funtion to obtain all of the metadata from my nd2 format files. However, when I run the function I get the following error messages:

No appropriate method, property, or field getMetadata for class
loci.formats.ChannelFiller

Error in ==> imreadBFmeta at 70
metadataList = r.getMetadata();

loci_tools is definitely in the right folder. Do you have any idea what could be wrong?

07 Aug 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl Elad

28 Jun 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl Christoph Moehl

I suggest to use the matlab function from openmicroscopy (see Curtis Ruedens post).

When I published imreadBF here, the original importer bfopen had some drawbacks. But this seems to be solved now.

14 Mar 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl Curtis Rueden

In response to the various questions being asked here: please try with the most up-to-date MATLAB script and documentation on the official site at:

https://www.openmicroscopy.org/site/support/bio-formats/users/matlab/

If you still have questions or issues, you will have better luck asking for help from the Bio-Formats developers on the OME mailing list (https://www.openmicroscopy.org/site/community/mailing-lists) or OME forums (https://www.openmicroscopy.org/community/).

29 Jan 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl David Verrelli

Sorry, I accidentally submitted twice.

I also want to ask/comment about two specific problems:

(1) Reading a uint8 file
I open a LIF file which should have intensities 0 to 255, I guess (unless the bit depth is higher???). However, the results returned from this M-file are in the range of int8, that is from -128 to +127. Looking at the frequency histogram, this is clearly wrong. I can fix it like this:
% Begin DIV edit 2013-01-22 %
if sgn == 0,
whos sgn arr
arr = uint8(arr >= 0) .* uint8(arr) + uint8(arr < 0) .* (uint8(arr + 128) + 128);
end;
% End DIV edit 2013-01-22 %

but I notice that the variable
sgn = loci.formats.FormatTools.isSigned(pixelType);
is already defined in the code, but never used for anything (see my previous post). Is there some bug there?

(2) Opening a LIF file
A Leica LIF file can contain multiple series. By default this code opens only the last series. I wonder if there is a way to access (in a controlled way) the other series in the file.

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