Web Log (Wlog) for the progress of Msc Project

Web Log (Wlog) of Msc Project

to keep a log of puny works done this summer, as a proof of existence

The log for each week consist of 3 parts:1. Current report of progress for this week 2. Things for discuss in this week’s weekly meeting 3. Plan for the next week

Week1

(Until 30 ^th, May)

• Briefly reviewed the based paper on SPIM-microPIV : ‘’3D + time blood flow mapping using SPIM-microPIV in the developing zebrafish heart’’
• Understand theoretically how light sheet microscopy and SPIM-microPIV works
• Discussed with supervisor to make clear the outline of works in the future

SPIM (Selective Plane Illumination Microscopy) PIV (Particle Image Velocimetry)

Week 2

(Until 6^th , June)

Due to personal reasons, there is no meeting, plan, or substantial progress this week

Week 3

(Until 13^th , June)

• Get familiar with the background knowledge of PIV and related python package
• Read paper introduce the core problem: “Out-of-focus effects on particle image visibility and correlation in microscopic particle image velocimetry”
• Learn to use GitHub as a version control tool to backup and manage the upcoming python code

week 4

(Until 22^th, June)

• get install and familiar with Jupyter lab, compile and run the tutorial code, read more in-depth with the related concept
• read paper related and prepare questions
• established several model of synthetic images showing particles moving
• read about and briefly analysed an old dataset about particle moving as “pipe flow”

week 5

(Until 27^th, June)

• generate a list of particles in same velocity
• generate particles in different velocities
• create a pipe flow model for PIV analysis
• review and analysis the correlation map

week 6

(Until 04^th, July)

• make clear how cross-correlation works
• list the primary objects to realize
• review some papers on depth of correlation, traditional methods and problems

plan to do:

• navigate the model of pipe by eye and try to reset the argument for better result
• try to change the source code for a different size of IW, not have to be square
• to find the relationship of correlation map from groups of particle and the whole image pair
• generate particles with different size and velocity to perform as in different layers
• get familiar with deconvolution
• do PIV challenge if possible

week 7

(Until 14^th, July)

The meeting this week is postponed to Friday

• failed to change or edit the source code
• generate model with considering of z-axis that particles can be different in size and have a velocity distribution on z-axis
• understand the basic of deconvolution and why to apply deconvolution on depth analysis

week 8

(Unitil 26^th, July)

• do works to realize the convolution and deconvolution
• debug the errors met for deconvolution
• prepare the presentation and made adjustment from the feedback

week 9

(Until 1^st, Aug)

• realize deconvolution of 3d images

• verify depth of effect to PIV, and deconvolution can help to improve performance of 3d image velocity analysis on z-axis

• transform the images to correlation matrix for further process

  should be discussed:

• how to determine the PSF for correlation matrix

• determine the process of deconvolve correlation matrix

• results in 3d image deconvolution

week 10

(Until 10^th, Aug)

• draw the heatmap of velocity distributed on y-z plane
• compare the result in velocity profile to show effect of deconvolution

Week 11

(Until 15^th, Aug)

• start writing the report on Overleaf
• try to debug the result shown in correlation Matrix deconvolve

Week 12

(Unitil 25^th, Aug)

• debug some part of correlation matrix
• halfly finished the report