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Merge pull request #713 from NEUBIAS/batch_processing
Batch processing
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<h4 id="batchshape"><a href="#batchshape">Batch analysis of nuclear shapes</a></h4> | ||
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- Download the input.zip containing the input images from [here](https://github.com/NEUBIAS/training-resources/tree/master/image_data/batch_process) and unpack to your course directory | ||
- In a previous module [there is a workflow to measure the shapes of nuclei in one image](https://neubias.github.io/training-resources/workflow_segment_2d_nuclei_measure_shape/index.html#2dnuclei) | ||
- Adapt this workflow for automated batch analysis of many images | ||
- Start by building the skeleton of the workflow without filling in the functionality; | ||
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Note that the code below runs fine, but does not produce any results: | ||
Note that the pseudo-code below will run fine, but does not produce any results: | ||
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``` | ||
def analyse(image_path, output_folder): | ||
print("Analyzing:", image_path) | ||
for image_path in image_paths: | ||
analyse(image_path, output_dir) | ||
FUNCTION analyse(image_path, output_folder) | ||
PRINT "Analyzing:", image_path | ||
END FUNCTION | ||
FOR each image_path in image_paths | ||
CALL analyse(image_path, output_dir) | ||
END FOR | ||
``` | ||
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- Make sure the loop with the (almost) empty analyse function runs without error before filling in the image analysis steps | ||
- Make sure the loop with the (almost) empty analyse function runs without error before filling in the image analysis steps | ||
- Inspect the analysis results in a suitable software |
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