image-analysis

This is a short script written to test different image analysis algorithms used in the lab.

Image cropping

Download the file using:

$ git clone https://github.com/microfluidix/image-analysis

By well

One calls the cropping function _cropAll(PATH,maskSize,wellSize,aspectRatio) from the library by calling import cropper in Jupyter Notebook.

The parameters are as follows:

• PATH: path to Images
• maskSize: size (um) of the mask
• wellSize: size (um) of the feature
• aspectRatio: um-to-px ratio

By spheroid

As above, one calls the cropping function _cropBySph(PATH,livePosition,wellSize,aspectRatio) from the library by calling import cropper in Jupyter Notebook.

The parameters are as follows:

• PATH: path to Images
• livePositon: channel of feature of interest (i.e. cell nuclei)
• wellSize: size (um) of the feature
• aspectRatio: um-to-px ratio