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[defaults]
# Using Galaxy roles only
roles_path = ./vendor

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#@UIService uiService
#@LogService log

# read in and display ImagePlus object(s)
from loci.plugins import BF
from loci.common import Region
from loci.plugins.in import ImporterOptions
from loci.plugins.util import LociPrefs
from ij import Prefs
from loci.formats import ImageReader

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west:
  team:
    - jburel
    - will-moore
    - dgault
    - manics
    - hflynn
    - pwalczysko
  releases:
    - name: OMERO 5.4.5

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bfCheckJavaPath;
r=bfGetReader(cellh5Path);

% Load full image
I0 = bfGetPlane(r,1);
sizeX = r.getSizeX();
sizeY = r.getSizeY();

% Load image in tiles
for n = [2 4 8 16]

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import java.io.IOException;

import loci.formats.FormatException;

import loci.formats.in.CellH5Reader;

public class CellH5Test {
    
    public static CellH5Reader reader;
    

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    // Legacy mode (default - 5.3.0 behavior)
    writer = new OMETiffWriter();
    writer.setMetadataRetrieve(omexml);
    // Write TIFFs in strips (no tiling)

    // Initial tile sizes
    iniTileSizeX = writer.getTileSizeX(); // returns sizeX
    iniTileSizeY = writer.getTileSizeY(); // returns sizeY

    // Set full image tiles

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<?xml version="1.0" encoding="UTF-8"?>
<OME UUID="urn:uuid:07504f88-7bc3-11e0-b937-2faf67bc00b3"
     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">
  <Image ID="Image:0" Name="5D image">
    <Pixels DimensionOrder="XYZCT" ID="Pixels:0:0" Type="int8" SizeC="3" SizeT="4" SizeX="128" SizeY="128" SizeZ="5">
      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
        <UUID FileName="plane.ome.tiff">urn:uuid:4978087c-a670-4b12-af53-256c62d8d101</UUID>

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import java.io.IOException;

import loci.common.services.DependencyException;

import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.services.OMEXMLService;
import loci.formats.FormatException;

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<?xml version="1.0" encoding="UTF-8"?>
<OME UUID="urn:uuid:07504f88-7bc3-11e0-b937-2faf67bc00b3"
     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">
  <Image ID="Image:0" Name="ROI with transforms">
    <Pixels DimensionOrder="XYZCT" ID="Pixels:0:0" Type="uint8" SizeC="1" SizeT="2" SizeX="512" SizeY="512" SizeZ="8">
      <Channel ID="Channel:0" SamplesPerPixel="1"/>
      <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">

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% Check Bio-Formats and initialize logging
bfCheckJavaPath();
bfInitLogging();

% Create a reader
r =  bfGetReader();

values = [true false];
for autostich = values
    for attachments = values