Code migrated to https://github.com/ome/ecdp2019-publication
Sébastien Besson sbesson
sbesson
/ bf_omero_build.sh
Last active
April 29, 2019 21:07
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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 |
sbesson
/ generate_tiff.py
Last active
December 13, 2018 14:55
See https://forum.image.sc/t/error-when-trying-to-write-ome-tiff-using-python-bioformats/21543
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| import bioformats.omexml as ome | |
| import javabridge as jv | |
| import bioformats | |
| import os | |
| import sys | |
| import numpy as np | |
| # Write file to disk | |
| def writeOMETIFF(img_XYCZT, path, type='uint16', verbose=True): |
sbesson
/ ansible.cfg
Last active
April 30, 2018 20:13
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| [defaults] | |
| # Using Galaxy roles only | |
| roles_path = ./vendor |
sbesson
/ czi.py
Last active
May 8, 2018 22:29
Related to https://github.com/openmicroscopy/bioformats/issues/2763
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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 |
sbesson
/ H1-2018.yml
Last active
March 14, 2018 10:02
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| west: | |
| team: | |
| - jburel | |
| - will-moore | |
| - dgault | |
| - manics | |
| - hflynn | |
| - pwalczysko | |
| releases: | |
| - name: OMERO 5.4.5 |
sbesson
/ CellH5_openBytes_test.m
Created
May 15, 2017 19:32
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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] |
sbesson
/ CellH5Test.java
Created
May 9, 2017 19:53
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| import java.io.IOException; | |
| import loci.formats.FormatException; | |
| import loci.formats.in.CellH5Reader; | |
| public class CellH5Test { | |
| public static CellH5Reader reader; | |
sbesson
/ TileWriter.java
Created
May 3, 2017 16:46
Proposals to fix the behavior of the 5.3.0 tiling API for full image tiles
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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 |
sbesson
/ multi-channel-4D-series.companion.ome
Last active
January 24, 2017 13:04
5D companion example
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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> |