Hosuk:LabNotes/2014-8-22: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Hosuki78
(Created page with "*LabNote ===Decoding with Agi26k0gap Padlock Probe : Masking images with MIP of all steps=== ====Masking==== *Done by Matt *MIP with images of all steps ...")
 
>Hosuki78
No edit summary
Line 7: Line 7:
*MIP with images of all steps
*MIP with images of all steps
*Run PISA of the MIP
*Run PISA of the MIP
seg_data = regionprops(MaskedFile,MaskedImgFile, 'MeanIntensity', 'Area', 'Centroid');
**seg_data = regionprops(MaskedFile,MaskedImgFile, 'MeanIntensity', 'Area', 'Centroid');




Line 21: Line 21:
**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.
**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====
*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====
*Each feature has Mean
*Image resolution : 20x obj, 4096 x 4086, z step = 1.04um  
*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
**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.
**eventually 63x obj.
====Result====
[[File:DecodeResultSummary_1_2014-08-21.png|600px]]

Revision as of 22:49, 22 August 2014


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');



Variables

  • 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

  • Each feature has Mean
  • 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.


Result

File:DecodeResultSummary 1 2014-08-21.png