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Measure Image Focus
The implementation of this plugin is described in and the URL for this page is linked from this paper:
Yang, S. J., Berndl, M., Ando, D. M., Barch, M., Narayanaswamy, A. , Christiansen, E., Hoyer, S., Roat, C., Hung, J., Rueden, C. T., Shankar, A., Finkbeiner, S., & and Nelson, P. (2018). Assessing microscope image focus quality with deep learning. BMC Bioinformatics, 19(1). [PDF]
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Install CellProfiler from source Using a terminal (found in Applications) and by running given commands in command line (instructions)
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Get CellProfiler Plugin. In the terminal, run these commands:
MYDIR=/tmp/; cd MYDIR
git clone https://github.com/CellProfiler/CellProfiler-plugins.git
cd CellProfiler-plugins/
- Install dependencies. In the terminal, run
pip install -r requirements.txt
- To run CellProfiler, in the terminal run the following; note you may get import errors, but these can be safely ignored:
cellprofiler --plugins-directory MYDIR/CellProfiler-plugins
Not yet supported.
Not yet supported because the only Tensorflow package available on Windows uses Python 3.
- In CellProfiler, Click "Images" and drag in images of interest [1]
- Edit > Add Module > Measurement > MeasureImageFocus
- Click on the module and in the module window choose Image > DNA (or name of image of interest)
- To test module on a single image, click “Test Mode” and then click the step button or
- "Analyze Images" to run module on all images
Note: the first time it's run, this module needs to download the model/weights, which can take a while.
[1] Download the test images from https://storage.googleapis.com/microscope-image-quality/static/fiji_plugin_test_images.zip. These images were excluded from the train dataset; the 6 focus examples were randomly selected and the other 2 examples show special cases.