![]() ![]() For ImageJ, we used an already developed macro designed to identify particles and quantify their area, and for CellProfiler, we developed a new analysis pipeline. For the lipid droplet analysis, we used two approaches, the free online computer software of reference, ImageJ, and another free online computer software, CellProfiler. Therefore, the aims of this study were to develop an accurate, standardized approach to quantify lipid droplet size of mature adipocytes and a clustering approach to analyze the total lipid content per adipocyte. Nutrition, stress, or chemical exposure can dysregulate adipogenic differentiation and lipid metabolism. However, imaging tools for evaluating intracellular lipid droplets remain at their infancy. During differentiation, neutral lipids that accumulate in adipocytes can be detected using stains and used as an index of cell differentiation. # The workspace object has access to the measurements # and the image set/image set list which can be used # to use/view/store/whatever output data.Adipogenic differentiation is the process by which preadipocytes become mature adipocytes, cells that store energy and regulate metabolic homeostasis. # Yes, we really do have to create a new workspace for each module # because the module attribute is required. group_number = 1 # Run the modules! workspace = None for module in pipeline. ![]() # We can only run one group - set the group index to 1. # Persist the object set here (for now, see workspace TODO) object_set = cellprofiler. # Create the image set, and add the image data image_set_list = cellprofiler. # Create and load the pipeline pipeline = cellprofiler. :param output_dir: (str) name of directory to store result in /data :param output_prefix: (str) the prefix of the output csv files :return """ # Run without the gui. ccpipe file (e.g.,test.cppipe) :param file_list: (list) list of absolute file paths. """Apply a CellProfiler pipeline file to a set of images. # Code adapted from def run_pipeline( pipeline_name, file_list, output_dir, output_prefix): Pipeline_filename = root+"ExampleFly.cppipe" # This should match what NamesAndTypes would produce. Root = "C:/Users/mayda/PycharmProjects/notebooks/Bio/CellProfiler/CellProfiler/cellprofiler/data/examples/ExampleFly/" # to use/view/store/whatever output data. # and the image set/image set list which can be used # The workspace object has access to the measurements # because the module attribute is required. # Yes, we really do have to create a new workspace for each module # Persist the object set here (for now, see workspace TODO) Image_set.add(image_name, (input_pixels)) Image_set = image_set_list.get_image_set(0)įor image_name, input_pixels in image_eritems(): # Create the image set, and add the image data (os.path.abspath('./CellProfiler/cellprofiler/utilities'))ĭef run_pipeline(pipeline_filename, image_dict): (os.path.abspath('./CellProfiler/cellprofiler')) Print ("exists: " if os.path.isfile(path) else "missing: ") + path Javabridge.class_for_name("")Ĭlasspath = javabridge.JClassWrapper('').getProperty('') Javabridge.start_vm(class_path=bioformats.JARS+) Result = self]įile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\utilities\hdf5_dict.py", line 379, in _getitem_Īssert feature_exists, "Feature does not exist".format(feature_name, object_name)ĪssertionError: Feature ImageSet_ImageSet for Image does not exist Vals = self.hdf5_dictįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\utilities\hdf5_dict.py", line 374, in _getitem_ Workspace = run_pipeline(pipeline_filename, images)įile "C:/Users/mayda/PycharmProjects/notebooks/Bio/CellProfiler/Testing.py", line 75, in run_pipelineįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\modules\namesandtypes.py", line 1731, in runįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\modules\**namesandtypes.py**", line 1663, in get_imagesetīlob = mįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\measurement.py", line 368, in _getitem_įile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\measurement.py", line 963, in get_measurement File "C:/Users/mayda/PycharmProjects/notebooks/Bio/CellProfiler/Testing.py", line 94, in ![]()
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