Hosuk:LabNotes/2014-8-22
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Decoding with Agi26k0gap Padlock Probe : Masking images with MIP of all steps
Masking
- Done by Matt
- MIP with images of all steps
- Run PISA of the MIP
seg_data = regionprops(MaskedFile,MaskedImgFile, 'MeanIntensity', 'Area', 'Centroid');
- Matlab scripts
- PISA_MaskImages_4d.m
- masking, and get mean intensity, area, (x, y) position
- normalize mean intensity of each dye using norm_tetra_3.m
- Plotting_3.m : Plot cloud plot
- norm_tetra_3.m : normalize intensity (sqrt...),
- tetrahedron_4.m : Plot 3(or 4) colors on tetrahedron space
- http://arep.med.harvard.edu/Polonator/2006/image_processing_pipeline/DATASETS/
- http://www.sciencemag.org/content/suppl/2005/10/12/1117389.DC1/Shendure.SOM.pdf
- The server hosting the source code no longer exists. The "newer" version of the software was written in C (http://arep.med.harvard.edu/Polonator/2006/image_processing_pipeline/). Not sure whether that's something you can pick up immediately.
- Image resolution : 20x obj, 4096 x 4086, z step = 1.04um
- Since how many features would be detected or how much dense rolonies in this sample, so image in wide field of view
- eventually 63x obj.