Mercurial > repos > imgteam > bioformats2raw
changeset 0:4b6c2135e547 draft
planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bf2raw.xml Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,133 @@ +<tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>with Bioformats</description> + <macros> + <token name="@TOOL_VERSION@">0.7.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <requirements> + <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container> + </requirements> + <command><![CDATA[ + +if [ ! -d $output.extra_files_path ];then + mkdir -p $output.extra_files_path; +fi; + +#if str($io_options.input.ext)=='html': + #set dirlist=os.listdir($io_options.input.extra_files_path) + #assert len($dirlist) > 0 + #set input_path=os.path.join(str($io_options.input.extra_files_path), str($dirlist[0])) +#else: + #set input_path=$io_options.input +#end if + +bioformats2raw $input_path $output.extra_files_path/$io_options.output_name +#if $bf2raw_params.multiscales['options'] == 'auto': + --target-min-size $bf2raw_params.multiscales.min_xy_size +#elif $bf2raw_params.multiscales['options'] == 'manual': + --resolutions $bf2raw_params.resolutions +#end if +--tile_height $bf2raw_params.tile_height +--tile_width $bf2raw_params.tile_width +--chunk_depth $bf2raw_params.chunk_depth +--downsample-type $bf2raw_params.downsample_type +--compression $bf2raw_params.compression +--max_workers "\${GALAXY_SLOTS:-4}" +$bf2raw_params.nesting +$bf2raw_params.omefolder +$bf2raw_params.droptop +#if not str($bf2raw_params.dimension_order) == 'keep input order': + --dimension-order $bf2raw_params.dimension_order +#end if +###--overwrite +--debug off &> /dev/null; + + ]]></command> + <inputs> + <section name="io_options" title="Input-output paths"> + <param name="input" type="data" format="atsf,scn,ali,labels,ffr,jpeg,ndpi,tf8,pty,fff,mnc,vms,mng,xml,pcx,img,pct,ims,bip,ome.xml,bin,flex,his,hdr,mov,psd,spi,ipl,dv,aiix,j2kr,pst,mod,ome.tif,tif,obf,dib,dic,im3,tga,pbm,c01,crw,mrcs,l2d,seq,mdb,cfg,htm,mvd2,arf,vsi,companion.ome,htd,aim,fts,ndpis,r3d.log,nef,res,jpx,ics,rec,nd2,cr2,dcm,mea,ome,lei,lms,j2k,oib,mtb,ima,ets,wlz,pict,sm3,sm2,nrrd,xdce,acff,al3d,zvi,1sc,xys,tiff,pgm,pcoraw,ppm,ipm,set,cxd,ipw,apl,fake,tnb,txt,xv,tf2,ps,log,zip,epsi,j2ki,dicom,top,msr,frm,hed,gif,dm2,dm3,dm4,zpo,wav,wat,2fl,sdt,liff,hx,pic,ome.btf,am,bmp,pnl,r3d_d3d,jpf,png,tfr,dti,nii.gz,cif,fdf,grey,df3,stk,fli,hdf,btf,stp,ch5,v,sld,ids,dv.log,jpk,mrw,r3d,xlog,ano,jpe,sxm,jpg,vws,raw,czi,spl,avi,ome.tf8,inf,spc,ome.tf2,spe,lsm,afm,lif,naf,afi,inr,lim,nd,tim,html,sif,env,tif,csv,map,nii,gel,ome.tiff,oif,par,amiramesh,pr3,fits,lut,jp2,oir,dat,aisf,zfr,zfp,xqd,eps,xqf,st,nhdr,i2i,thm,exp,svs,mrc" label="Input image located in Galaxy history"/> + <param name="output_name" type="text" value="data.zarr" label="Output zarr data"/> + </section> + <section name="bf2raw_params" title="Parameters fed to file conversion module"> + <conditional name="multiscales" > + <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" > + <option value="auto" selected="true">auto</option> + <option value="manual" selected="false">manual</option> + </param> + <when value="auto"> + <param name="min_xy_size" type="integer" min="1" optional="true" label="Min x-y dimension for the lowest resolution" value="256" /> + </when> + <when value="manual"> + <param name="resolution_count" type="integer" min="1" optional="true" label="Number of resolution layers" value="3"/> + </when> + </conditional > + <param name="tile_height" type="integer" label="Tile height" value="96" min="1" /> + <param name="tile_width" type="integer" label="Tile width" value="96" min="1" /> + <param name="chunk_depth" type="integer" label="Chunk depth" value="1" min="1" /> + <param name="downsample_type" type="select" label="Downsampling method" multiple="false" > + <option value="SIMPLE" selected="true">SIMPLE</option> + <option value="GAUSSIAN" selected="false">GAUSSIAN</option> + <option value="AREA" selected="false">AREA</option> + <option value="LINEAR" selected="false">LINEAR</option> + <option value="CUBIC" selected="false">CUBIC</option> + <option value="LANCZOS" selected="false">LANCZOS</option> + </param> + <param name="compression" type="select" label="Compression method" multiple="false" > + <option value="null" selected="false">null</option> + <option value="zlib" selected="false">zlib</option> + <option value="blosc" selected="true">blosc</option> + </param> + <param name="dimension_order" type="select" label="Dimension order" multiple="false"> + <option value="keep input order" selected="true">keep input order</option> + <option value="XYZCT" selected="false">XYZCT</option> + <option value="XYZTC" selected="false">XYZTC</option> + <option value="XYCTZ" selected="false">XYCTZ</option> + <option value="XYCZT" selected="false">XYCZT</option> + <option value="XYTCZ" selected="false">XYTCZ</option> + <option value="XYTZC" selected="false">XYTZC</option> + </param> + <param name="nesting" type="boolean" label="Use ' / ' as chunk path separator" truevalue="" falsevalue="--no-nested" checked="true" /> + <param name="omefolder" type="boolean" label="Export OME metadata" truevalue="" falsevalue="--no-ome-meta-export" checked="true" /> + <param name="droptop" type="boolean" label="Drop the series layer in the OME-Zarr folder hierarchy" truevalue="--scale-format-string '%2$d'" falsevalue="" checked="false" /> + </section> + </inputs> + <outputs> + <data name="output" format="html" label="OME-Zarr Output" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="xyz_8bit__mitotic_plate_calibrated.tif"/> + <param name="output_name" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr" /> + <output name="output" ftype="html"> + <extra_files type="file" name="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" /> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input" value="astronaut.png"/> + <param name="output_name" value="astronaut.ome.zarr" /> + <output name="output" ftype="html"> + <extra_files type="file" name="astronaut.ome.zarr/.zgroup" value="astronaut.ome.zarr/.zgroup" /> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input" value="rocket.jpg"/> + <param name="output_name" value="rocket.ome.zarr" /> + <output name="output" ftype="html"> + <extra_files type="file" name="rocket.ome.zarr/.zattrs" value="rocket.ome.zarr/.zattrs" /> + </output> + </test> + </tests> + <help> +**What it does** + +Bioformats-based tool that converts a wide range of image file formats to the cloud-optimised format OME-Zarr following the `OME-NGFF`_ specification. + +.. _OME-NGFF: https://ngff.openmicroscopy.org/latest + </help> + <citations> + <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "bioformats2raw.layout" : 3 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/0/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,92 @@ +{ + "multiscales" : [ { + "metadata" : { + "method" : "loci.common.image.SimpleImageScaler", + "version" : "Bio-Formats 6.13.0" + }, + "axes" : [ { + "name" : "t", + "type" : "time" + }, { + "name" : "c", + "type" : "channel" + }, { + "name" : "z", + "type" : "space" + }, { + "name" : "y", + "type" : "space" + }, { + "name" : "x", + "type" : "space" + } ], + "name" : "astronaut.png", + "datasets" : [ { + "path" : "0", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 1.0, 1.0 ], + "type" : "scale" + } ] + }, { + "path" : "1", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 2.0, 2.0 ], + "type" : "scale" + } ] + }, { + "path" : "2", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 4.0, 4.0 ], + "type" : "scale" + } ] + } ], + "version" : "0.4" + } ], + "omero" : { + "channels" : [ { + "color" : "FF0000", + "coefficient" : 1, + "active" : true, + "label" : "Channel 0", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + }, { + "color" : "00FF00", + "coefficient" : 1, + "active" : true, + "label" : "Channel 1", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + }, { + "color" : "0000FF", + "coefficient" : 1, + "active" : true, + "label" : "Channel 2", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + } ], + "rdefs" : { + "defaultT" : 0, + "model" : "color", + "defaultZ" : 0 + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/0/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/0/0/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 480, 640 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 3, 1, 480, 640 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/0/1/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 240, 320 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 3, 1, 240, 320 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/0/2/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 120, 160 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 3, 1, 120, 160 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/OME/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "series" : [ "0" ] +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/OME/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/astronaut.ome.zarr/OME/METADATA.ome.xml Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,1 @@ +<?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"><Image ID="Image:0" Name="astronaut.png"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="true" SignificantBits="8" SizeC="3" SizeT="1" SizeX="640" SizeY="480" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "bioformats2raw.layout" : 3 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/0/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,92 @@ +{ + "multiscales" : [ { + "metadata" : { + "method" : "loci.common.image.SimpleImageScaler", + "version" : "Bio-Formats 6.13.0" + }, + "axes" : [ { + "name" : "t", + "type" : "time" + }, { + "name" : "c", + "type" : "channel" + }, { + "name" : "z", + "type" : "space" + }, { + "name" : "y", + "type" : "space" + }, { + "name" : "x", + "type" : "space" + } ], + "name" : "rocket.jpg", + "datasets" : [ { + "path" : "0", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 1.0, 1.0 ], + "type" : "scale" + } ] + }, { + "path" : "1", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 2.0, 2.0 ], + "type" : "scale" + } ] + }, { + "path" : "2", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 1.0, 4.0, 4.0 ], + "type" : "scale" + } ] + } ], + "version" : "0.4" + } ], + "omero" : { + "channels" : [ { + "color" : "FF0000", + "coefficient" : 1, + "active" : true, + "label" : "Channel 0", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + }, { + "color" : "00FF00", + "coefficient" : 1, + "active" : true, + "label" : "Channel 1", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + }, { + "color" : "0000FF", + "coefficient" : 1, + "active" : true, + "label" : "Channel 2", + "window" : { + "min" : 0.0, + "max" : 255.0, + "start" : 0.0, + "end" : 255.0 + }, + "family" : "linear", + "inverted" : false + } ], + "rdefs" : { + "defaultT" : 0, + "model" : "color", + "defaultZ" : 0 + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/0/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/0/0/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 427, 640 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 3, 1, 427, 640 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/0/1/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 213, 320 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 3, 1, 213, 320 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/0/2/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 106, 160 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 3, 1, 106, 160 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/OME/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "series" : [ "0" ] +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/OME/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rocket.ome.zarr/OME/METADATA.ome.xml Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,1 @@ +<?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"><Image ID="Image:0" Name="rocket.jpg"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="640" SizeY="427" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "bioformats2raw.layout" : 3 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/.zattrs Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,64 @@ +{ + "multiscales" : [ { + "metadata" : { + "method" : "loci.common.image.SimpleImageScaler", + "version" : "Bio-Formats 6.13.0" + }, + "axes" : [ { + "unit" : "second", + "name" : "t", + "type" : "time" + }, { + "name" : "c", + "type" : "channel" + }, { + "unit" : "micrometer", + "name" : "z", + "type" : "space" + }, { + "unit" : "micrometer", + "name" : "y", + "type" : "space" + }, { + "unit" : "micrometer", + "name" : "x", + "type" : "space" + } ], + "name" : "xyz_8bit__mitotic_plate_calibrated.tif", + "datasets" : [ { + "path" : "0", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 3.0, 0.08519643016734027, 0.08519643016734027 ], + "type" : "scale" + } ] + }, { + "path" : "1", + "coordinateTransformations" : [ { + "scale" : [ 1.0, 1.0, 3.0, 0.17039286033468054, 0.17039286033468054 ], + "type" : "scale" + } ] + } ], + "version" : "0.4" + } ], + "omero" : { + "channels" : [ { + "color" : "808080", + "coefficient" : 1, + "active" : true, + "label" : "Channel 0", + "window" : { + "min" : 3.0, + "max" : 162.0, + "start" : 3.0, + "end" : 162.0 + }, + "family" : "linear", + "inverted" : false + } ], + "rdefs" : { + "defaultT" : 0, + "model" : "greyscale", + "defaultZ" : 3 + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/.zgroup Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,3 @@ +{ + "zarr_format" : 2 +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/.zarray Wed Nov 15 15:14:17 2023 +0000 @@ -0,0 +1,17 @@ +{ + "chunks" : [ 1, 1, 1, 263, 263 ], + "compressor" : { + "clevel" : 5, + "blocksize" : 0, + "shuffle" : 1, + "cname" : "lz4", + "id" : "blosc" + }, + "dtype" : "|u1", + "fill_value" : 0, + "filters" : null, + "order" : "C", + "shape" : [ 1, 1, 6, 263, 263 ], + "dimension_separator" : "/", + "zarr_format" : 2 +} \ No newline at end of file
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