Hosuk:LabNotes/2014-8-22
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Decoding with Agi26k0gap Padlock Probe : Masking images with MIP of all steps[edit]
Masking[edit]
- 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.
Variables[edit]
- After masking
- DecodeInfoMaxNum : Total number of features by regionprops
- DecodeInfo_MeanIntensity(1:MaxRolonyNum, 1:NumOfSteps) : Mean intensity of each feature
- RolonyInfo_Area(1:MaxRolonyNum, 1): Area(number of pixels) of each feature
- RolonyInfo_CenterY(1:MaxRolonyNum, 1) : Centroid X of each feature
- RolonyInfo_CenterX(1:MaxRolonyNum, 1): Centroid Y of each feature
- After normalize
- Max_MeanIntensity(1:MaxRolonyNum, 1) : Max intensity of each Step1 ~ Step21
- DecodeInfo_NormMeanIntensity(1:MaxRolonyNum, 1:NumOfSteps) : Normalized by Max
- DecodeInfo_NormMeanIntensity = DecodeInfo_MeanIntensity / Max_MeanIntensity;
- DecodeInfo_Sqrt(1:DecodeInfoMaxNum, 1:NumOfDecodingSlots) : sqrt of sum of sq of each intensity = sqrt[ (I_488)^2 + (I_Cy3)^2 + (I_Cy5)^2 ]
- DecodeInfo_NormMeanIntensity2(1:MaxRolonyNum, 1:NumOfSteps) : norm intensity after filtered out the weak signal
- all intensity = 0 when DecodeInfo_Sqrt < thresh_val (it is 0.1 for now)
- DecodeInfo_NormMeanIntensity_Result(1:MaxRolonyNum, 1:NumOfSteps) : normalized again by norm_tetra_3, plot cloud with this
- [DecodeInfo_NormMeanIntensity_Result, cms, calls, coords_3d] = norm_tetra_3(DecodeInfo_NormMeanIntensity2, NumOfSteps, thresh_subvalue);
Normalized intensity distribution[edit]
- all intensity = 0 when DecodeInfo_Sqrt < thresh_val
- Blue : 488, Green : Cy3, Red : Cy5
File:DecodeResult CloudPlots 2014-08-21.png
Result[edit]
File:DecodeResultSummary 1 2014-08-21.png
File:DecodeResult MappedfeatureTo1stROolony 2014-08-21.png
File:DecodeResult MappedfeatureToBF 2014-08-21.png