GitLab

Add combinechannels.py. Tested on Sandhya's images and runs correctly. rescaletif.py still not fully implemented.

Fix artifact in writing condensate_masks_color image where the corner of the droplet bounding box overlays green on top of red or blue pixels by zeroing green value in all pixels where red or blue value is greater than zero.

Implement writing a diagnostic image where each grayscale image at the dense-phase z-plane is shown with a color overlay showing dense phase in red and dilute phase in blue, change dilutemaskinnerradius default to 2 pixels, implement asking user whether to overwrite existing directories.

Fix very stupid error regarding indentation of io.imsave() calls relative to the loops they are nested in. Script runs much faster now. Implement writing an output .csv with image acquisition parameters. v0.2

Finish implenting lif2tif.py. Runs and gives output for all image types tested, and appears to give identical results for xyz 3-color tilescan images as compared with Fiji bioformats importer. v0.1.

Show default values with --help argument, make several parameters configurable on the command line, make rolling ball background subtraction optional and turned off by default, change distance transform threshold argument to an absolute number rather than a percentage threshold, implement returning mean intensity over the entire droplet. Start work on .lif file processor. v0.2

Finish implementation of all functions required for basic segmentation, dense/dilute phase intensity measurement, dense phase volume measurement, and saving data. Runs without errors, but seems to be giving spuriously high dense phase intensities in the red channel.

Continue implementing dense and dilute phase mask generation and intensity value calculations. Not complete, not tested.

Partially implement dense and dilute phase mask generation and intensity value calculations. Not complete, not tested.