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#!/usr/bin/env python
# Generate companion files for the TIFF files of the
# first sample dataset of EMPIAR-11537 available from
# https://ftp.ebi.ac.uk/empiar/world_availability/11537/data/4G_Run%201/

import re
import sys
import uuid
import xml.etree.ElementTree as ET

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<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 6.6.0" UUID="urn:uuid:d830ec74-9e12-43cd-b4d0-0a0c8a7c57c4" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
   <Image ID="Image:0" Name="test">
      <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" Type="uint8" PhysicalSizeX="1" PhysicalSizeXUnit="µm">
         <Channel ID="Channel:0:0" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
            <UUID FileName="test.ome.tiff">urn:uuid:faa8214a-e188-4fb7-bb85-262225e6bfb4</UUID>
         </TiffData>

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#! /usr/bin/env python
from github import Github

gh = Github()
r = gh.search_code('org:ome filename:.travis.yml')
repos = sorted(set([i.repository.html_url for i in r]))

for repo in repos:
  print(repo)

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<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06
                         http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">

  <Plate
     ID="Plate:0"
     Name="Control Plate"
     ColumnNamingConvention="letter"

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writer = loci.formats.out.PyramidOMETiffWriter();

I0 = imread('rice.png');
I = cell(3,1);
I{1} = imresize(I0, 8);
I{2} = imresize(I0, 4);
I{3} = imresize(I0, 2);
I{4} = I0;

metadata = createMinimalOMEXMLMetadata(I{1});

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Attribution 4.0 International

=======================================================================

Creative Commons Corporation ("Creative Commons") is not a law firm and
does not provide legal services or legal advice. Distribution of
Creative Commons public licenses does not create a lawyer-client or
other relationship. Creative Commons makes its licenses and related
information available on an "as-is" basis. Creative Commons gives no
warranties regarding its licenses, any material licensed under their

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/data/OMERO/ManagedRepository/demo_2/2017-08/14/10-23-19.875/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24277.screen
/data/OMERO/ManagedRepository/demo_2/2017-08/14/10-59-37.469/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24280.screen
/data/OMERO/ManagedRepository/demo_2/2017-08/14/13-40-38.086/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24294.screen
/data/OMERO/ManagedRepository/demo_2/2017-08/14/15-17-49.614/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24295.screen
/data/OMERO/ManagedRepository/demo_2/2017-08/14/16-51-36.693/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24296.screen
/data/OMERO/ManagedRepository/demo_2/2017-08/14/18-30-38.408/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24300.screen
/data/OMERO/ManagedRepository/demo_2/2017-08/14/20-13-38.290/tmp/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24301.screen
/data/OMERO/ManagedRepository/demo_2/2017-08

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#! /usr/bin/env python
# Remove obsolete integration branches

import scc.git
import sys

# Login and check the organization
gh = scc.git.get_github(scc.git.get_token())
print "Authenticated as %s" % gh.get_user().login
branch = sys.argv[1]

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#
git clone https://github.com/snoopycrimecop/bio-formats-build -b east_merge_trigger
pushd bio-formats-build
git submodule update --init
pushd bioformats
popd
docker build -t bf --build-arg BUILD_IMAGE=gradle:jdk8 .
popd

git clone https://github.com/snoopycrimecop/omero-build -b west_merge_trigger

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Code migrated to https://github.com/ome/ecdp2019-publication