hack_rcpnl_metadata.md

Tools

1. convert .rcpnl file to .ome.tif using
   bfconvert sample.rcpnl sample.ome.tif

2. extract XML from converted .ome.tif file using
   tiffcomment sample.ome.tif > output_metadata.xml

3. edit output_metadata.xml using text editor

4. overwrite the metadata of sample.ome.tif using tiffcomment
tiffcomment -set 'newmetadata.xml' sample.ome.tif

make_ometiff_xml.py

# Using bftool to extract the xml
# adjust ram limit for larger file
# set BF_MAX_MEM=80g
# bftools\showinf.bat -omexml -nopix -novalid "Scan_20200929_094137_01x4x01180.rcpnl" > "Scan_20200929_094137_01x4x01180.rcpnl.xml"
# Manually cleanup the xml using text editor

from ashlar import reg
import skimage.io

c1r = reg.BioformatsReader('Scan_20200929_094137_01x4x01180.rcpnl')

kwargs_first = dict(
    photometric='minisblack', metadata=None, bigtiff=True,
    description='!!xml!!', append=True, check_contrast=False
)
kwargs_rest = kwargs_first.copy()
del kwargs_rest['description']
num_images = 772
out_name = 'Scan_20200929_094137_01x4x0{:04}.ome.tif'.format(num_images)

for i in range(num_images):
    if i % 50 == 0:
        print(i)
    for j in range(4):
        img = c1r.read(i, j)
        k = kwargs_rest
        if i == 0 and j == 0:
            k = kwargs_first
        skimage.io.imsave(out_name, img, **k)


import xml.etree.ElementTree as ET

image_el = '''
<Image ID="Image:{image_num}" Name="{name} #{series}">
    <InstrumentRef ID="Instrument:0" />
    <ObjectiveSettings ID="Objective:0" />
    <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:{image_num}" Interleaved="false"
        PhysicalSizeX="0.32499998807907104" PhysicalSizeXUnit="\xb5m" PhysicalSizeY="0.32499998807907104"
        PhysicalSizeYUnit="\xb5m" PhysicalSizeZ="1.0" PhysicalSizeZUnit="\xb5m" SignificantBits="16" SizeC="4"
        SizeT="1" SizeX="2560" SizeY="2160" SizeZ="1" Type="uint16">
        <Channel EmissionWavelength="431.0" EmissionWavelengthUnit="nm" ExcitationWavelength="395.0"
            ExcitationWavelengthUnit="nm" ID="Channel:{image_num}:0" NDFilter="0.0" SamplesPerPixel="1">
            <LightPath />
        </Channel>
        <Channel EmissionWavelength="525.0" EmissionWavelengthUnit="nm" ExcitationWavelength="485.0"
            ExcitationWavelengthUnit="nm" ID="Channel:{image_num}:1" NDFilter="0.0" SamplesPerPixel="1">
            <LightPath />
        </Channel>
        <Channel EmissionWavelength="590.0" EmissionWavelengthUnit="nm" ExcitationWavelength="555.0"
            ExcitationWavelengthUnit="nm" ID="Channel:{image_num}:2" NDFilter="0.0" SamplesPerPixel="1">
            <LightPath />
        </Channel>
        <Channel EmissionWavelength="690.0" EmissionWavelengthUnit="nm" ExcitationWavelength="651.0"
            ExcitationWavelengthUnit="nm" ID="Channel:{image_num}:3" NDFilter="0.0" SamplesPerPixel="1">
            <LightPath />
        </Channel>
    </Pixels>
</Image>

'''

tiffdata_el = '''
<T>
    <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="{aa}" PlaneCount="1">
        <UUID FileName="{filename}">{uuid}</UUID>
    </TiffData>
    <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="{bb}" PlaneCount="1">
        <UUID FileName="{filename}">{uuid}</UUID>
    </TiffData>
    <TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="{cc}" PlaneCount="1">
        <UUID FileName="{filename}">{uuid}</UUID>
    </TiffData>
    <TiffData FirstC="3" FirstT="0" FirstZ="0" IFD="{dd}" PlaneCount="1">
        <UUID FileName="{filename}">{uuid}</UUID>
    </TiffData>
</T>
'''
ET.register_namespace('', 'http://www.openmicroscopy.org/Schemas/OME/2016-06')

root = ET.fromstring(open(r'D:\yc296\20201011-CCR-092020-PDAC-TMA2\Scan_20200929_094137_01x4x01180.rcpnl.xml').read())
plane_el = list(root.iter('{http://www.openmicroscopy.org/Schemas/OME/2016-06}Plane'))

for e in plane_el:
    e.set('TheT', '0')

import uuid
img_uuid = uuid.uuid4().urn

root.remove(root[1])

for i in range(num_images):
    img_el = ET.fromstring(image_el.format(image_num=i, name=out_name, series=i+1))
    aa, bb, cc, dd = list(range(i*4, (i+1)*4))
    tiff_el = ET.fromstring(tiffdata_el.format(filename=out_name, uuid=img_uuid, aa=aa, bb=bb, cc=cc, dd=dd))
    img_el[2].extend(tiff_el[:])
    img_el[2].extend(plane_el[i*4:(i+1)*4])
    root.append(img_el)

root.set('UUID', img_uuid)
ET.ElementTree(root).write('{}.xml'.format(out_name), encoding='utf-8', xml_declaration=True)


# Using bftool to inject the xml
# bftools\tiffcomment.bat -set "Scan_20200929_094137_01x4x00772.ome.tif.xml" "Scan_20200929_094137_01x4x00772.ome.tif"

Using the correct character is required for a valid ome-xml - μm