gimp script to batch invert

test-batch-invert.py

#!/usr/bin/env python
#
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# Copyright (c) 2013, Jose F. Maldonado
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import os
from gimpfu import *

def batch_invert(img, layer, inputFolder, outputFolder):
    ''' Inverts the colors of the PNG and JPEG images of a folder.
    
    Parameters:
    img : image The current image (unused).
    layer : layer The layer of the image that is selected (unused).
    inputFolder : string The folder of the images that must be inverted.
    outputFolder : string The folder in which save the inverted images.
    '''
    # Iterate the folder
    for file in os.listdir(inputFolder):
        try:
            # Build the full file paths.
            inputPath = inputFolder + "\\" + file
            outputPath = outputFolder + "\\" + file
        
            # Open the file if is a JPEG or PNG image.
            image = None
            if(file.lower().endswith(('.png'))):
                image = pdb.file_png_load(inputPath, inputPath)
            if(file.lower().endswith(('.jpeg', '.jpg'))):
                image = pdb.file_jpeg_load(inputPath, inputPath)
                
            # Verify if the file is an image.
            if(image != None):
                # Invert the image.
                if(len(image.layers) > 0):
                    layer = image.layers[0]
                    pdb.gimp_invert(layer)
                    
                    # Save the image.
                    if(file.lower().endswith(('.png'))):
                        pdb.file_png_save(image, image.layers[0], outputPath, outputPath, 0, 9, 0, 0, 0, 0, 0)
                    if(file.lower().endswith(('.jpeg', '.jpg'))):
                        pdb.file_jpeg_save(image, layer, outputPath, outputPath, 0.9, 0, 0, 0, "Creating with GIMP", 0, 0, 0, 0)
        except Exception as err:
            gimp.message("Unexpected error: " + str(err))

register(
    "python_fu_test_batch_invert",
    "Batch invert",
    "Inverts the colors of the PNG and JPEG images of a folder",
    "JFM",
    "Open source (BSD 3-clause license)",
    "2013",
    "<Image>/Filters/Test/Batch invert",
    "*",
    [
        (PF_DIRNAME, "inputFolder", "Input directory", ""),
        (PF_DIRNAME, "outputFolder", "Output directory", "")
    ],
    [],
    batch_invert)

main()

Put the .py file into the plugins folder (on windows for me it's C:\Users\USERNAME.gimp-2.8\plugins)

Then under the filters I have it under Test>batch invert then you should be able to go from there.