This is the OMERO script that is discussed on the forum at https://www.openmicroscopy.org/community/viewtopic.php?f=16&t=920, written by Pierre Pouchin.

Restore_colors.py

#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
This script tries to restore the colors for the selected LIF/LSM images.

@author Pierre Pouchin
<a href="mailto:[email protected]">[email protected]</a>
@version 4.3
"""

import omero
import omero.scripts as scripts
from omero.gateway import BlitzGateway
from omero.rtypes import *

PARAM_DATATYPE = "Data_Type"
PARAM_IDS = "IDs"
PARAM_ALL_IMAGES = "All_Images"

# Global dictionary of original file IDs
original_ids = {}

################################################################################
def getOriginalMetadata(img) :
    """
    Gets the original metadata of an image [loadOrginalMetadata() method is broken]

    @param img:    The ImageWrapper object
    """

    global_metadata = list()
    series_metadata = list()

    for ann in img.listAnnotations():
      if hasattr(ann, "file") and ann._obj.ns is not None and ann._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and \
                ann.getFile().getName() == omero.constants.annotation.file.ORIGINALMETADATA:
        t_file = list()
        for piece in ann.getFileInChunks():
          t_file.append(piece)
        temp_file = "".join(t_file).split('\n')
        flag = None
        for l in temp_file:
          if l.startswith("[GlobalMetadata]"):
            flag = 1
          elif l.startswith("[SeriesMetadata]"):
            flag = 2
          else:
            if len(l) < 1:
              l = None
            else:
              l = tuple(l.split("="))
            
            if l is not None:
              if flag == 1:
                global_metadata.append(l)
              else:
                series_metadata.append(l)

        return (ann, (global_metadata), (series_metadata))
    return None


def colorname2rgb(name) :
    """
    Gives the RGB code corresponding to a color name.
    
    @param name: The color name
    """

    name2rgb = dict()

    name2rgb['Red'] = (255,0,0)
    name2rgb['Green'] = (0,255,0)
    name2rgb['Blue'] = (0,0,255)
    name2rgb['Yellow'] = (255,255,0)
    name2rgb['Magenta'] = (255,0,255)
    name2rgb['Cyan'] = (0,255,255)
    name2rgb['Gray'] = (128,128,128)

    if name in name2rgb:
      return name2rgb[name]
    else:
      return (255,255,255)


def colorcode2rgb(integer) :
    """
    Gives the RGB value corresponding to an int color value.
    
    @param integer: The integer value of the color
    """

    #Integer corresponds to BGR in LSM files
    b = (integer & 16711680) >> 16
    g = (integer & 65280) >> 8
    r = (integer & 255)

    return (r,g,b)


def restore_image(conn, img, params) :
    """
    Restores the colors of one image

    @param conn:   The BlitzGateway connection
    @param img:    The ImageWrapper object
    @param params: The script parameters
    """

    treated = 0
    cNames = dict()
    cCodes = dict()

#    original method broken...
#    om = image.loadOriginalMetadata()
    om = getOriginalMetadata(img)

    if om is not None:
      #global_metadata : om[1]
      #series_metadata : om[2]
      for keyValue in om[2]:
        if len(keyValue) > 1:
          # LIF colors
          if keyValue[0].startswith("ChannelDescription|LUTName"):
            tmp_ar = keyValue[0].split(' ')
            cNames[int(tmp_ar[1])] = keyValue[1]
          # LSM colors
          if keyValue[0].startswith("DataChannel") and keyValue[0].endswith("Color"):
            tmp_ar = keyValue[0].split(' ')
            cCodes[int(tmp_ar[1].strip('#'))-1] = int(keyValue[1])

      if cNames:
        for index, c in enumerate(img.getChannels()):
          lc = c.getLogicalChannel()
          if index in cNames:
            r, g, b = colorname2rgb(cNames[index])
            cObj = conn.getQueryService().get("Channel", c.id)
            cObj.red = omero.rtypes.rint(r)
            cObj.green = omero.rtypes.rint(g)
            cObj.blue = omero.rtypes.rint(b)
            cObj.alpha = omero.rtypes.rint(255)
            conn.getUpdateService().saveObject(cObj)
        
        img.resetRDefs()
        treated = 1
      elif cCodes:
        for index, c in enumerate(img.getChannels()):
          lc = c.getLogicalChannel()
          if index in cCodes:
            r, g, b = colorcode2rgb(cCodes[index])
            cObj = conn.getQueryService().get("Channel", c.id)
            cObj.red = omero.rtypes.rint(r)
            cObj.green = omero.rtypes.rint(g)
            cObj.blue = omero.rtypes.rint(b)
            cObj.alpha = omero.rtypes.rint(255)
            conn.getUpdateService().saveObject(cObj)

        img.resetRDefs()
        treated = 1


    return treated

    
def run(conn, params):
    """
    Treats each image specified.
    
    @param conn:   The BlitzGateway connection
    @param params: The script parameters
    """
    print "Parameters = %s" % params

    images = []
    if params[PARAM_ALL_IMAGES]:
      images = list(conn.getObjects('Image'))
    else:
      objects = conn.getObjects(params[PARAM_DATATYPE], params[PARAM_IDS])
      if params[PARAM_DATATYPE] == 'Dataset':
        for ds in objects:
          images.extend( list(ds.listChildren()) )
      else:
        images = list(objects)
      
      # Remove duplicate images in multiple datasets
      seen = set()
      images = [x for x in images if x.id not in seen and not seen.add(x.id)]

    # Remove images which are not writable for the user
    images = [x for x in images if x.canWrite()]
    
    print("Processing %s image%s" % (len(images), len(images) != 1 and 's' or ''))
    
    count = 0 
    for img in images:
      treated = restore_image(conn, img, params)
      if(treated == 1):
        count += 1
    
    return count


def summary(count):
    """Produces a summary message (number of image(s) processed)"""
    msg = "%d image%s processed" % (count, count != 1 and 's' or '')
    return msg


def runAsScript():
    """
    The main entry point of the script, as called by the client via the 
    scripting service, passing the required parameters. 
    """
    dataTypes = [rstring('Dataset'),rstring('Image')]
    
    client = scripts.client('Restore_colors.py', """\
    Restores the original colors for LIF and LSM files.
    """, 
    
    scripts.String(PARAM_DATATYPE, optional=False, grouping="1.1",
        description="The data you want to work with.", values=dataTypes, 
        default="Image"),

    scripts.List(PARAM_IDS, optional=True, grouping="1.2",
        description="List of Dataset IDs or Image IDs").ofType(rlong(0)),

    scripts.Bool(PARAM_ALL_IMAGES, grouping="1.3", 
        description="Process all images (ignore the ID parameters)", 
        default=False),

    version = "1.0",
    authors = ["Pierre Pouchin", "GReD"],
    institutions = ["Universite d'Auvergne"],
    contact = "[email protected]",
    ) 
    
    conn = BlitzGateway(client_obj=client)
    
    # Process the list of args above. 
    params = {}
    for key in client.getInputKeys():
      if client.getInput(key):
        params[key] = client.getInput(key, unwrap=True)
    
    # Call the main script - returns the number of images and total bytes
    count = run(conn, params)
    
    if count >= 0:
      # Combine the totals for the summary message
      msg = summary(count)
      print msg
      client.setOutput("Message", rstring(msg))

if __name__ == "__main__":
    """
    Python entry point
    """
    runAsScript()