tonkin_lab

Code for Tonkin Lab data

cTonkin_montageMaker.ijm

Create a consistent montage from multi-channel data.

Options

• File to montage
• Output path to save montage to
• Ch1-5 colours, false colour for each channel
• ROI Size - Side length of roi to montage
• Add scale bar
• Length of scale bar

cTonkin_radial_intensity_measure.ijm

Measre mean radial intensity of cells

Options

• Input file (ignored if batch is selected)
• Output path - where to put results
• Width of "edge" - how many micron to step output edge in from edge of detected region
• Expand boundary from paraistes - Segmentation is done by thresholding parasite channel, edge of the vacuole is defined by expanding this area
• Get radial distribution - measure (and save) actual intensity distribution normalised from edge to centre
• Display graph - show radial distribution on screen
• Batch - Batch a directory instead of an individual file, will prompt for directory
• Allow multiple rois
• Print results on mask image - Prints the results on the mask image
• Parasite Masking Channel - Parasite channel for segmentation
• Measurement Channel - channel to be measured

Mode:

- Classic - will do the above
- Annotate - Will open each image and allow annotation, will skip file if there's already an annotation
- Analyse - Will open each image that has an associated annotation and perform analysis

Note for both analyse and annotate you need to specify the correct output path above which is where the annotations are stored.