final CL demo - develop

[xiyuyi]

Continued in #108

[xiyuyi]

• download all data
• initial check and confirm all files are correct
• organize dataset (convert to tiffs,
• identify and crop FOVs for 2 channel. keep the same for all dataset.
• identify 3D PSF stacks fro both colors)
  -------bead coordinates: NW_astig_spetrum_data\September2019_CS_3DsSMLM\Sep2019_bead_coordinates.xlsx
• crop PSF stacks automatically.
• identify target recovery region and set into individual frame images.
• wire up with PRIS recovery.
• find field distortion for the first channel.

[xiyuyi]

downloading data started at 11:16 am - 11:23.
11:23 organize a bit: kept the data in Ruby drive:
G:\DH_localization\Experiments_Phase2_afterSPIE\NW_astig_spetrum_data\September2019_CS_3DsSMLM
11:31 started to check data using jupyter notebook.
11:41 ---- issue: no nd2reader. installed separately. assigned an issue to Xingjia.
12:00 started working.
12:04 data is in slightly different format. go back and check everydataset, write notes in ppt, and organize.

[xiyuyi]

12:32. finished checking data. all in very good condition. now converting into tif for convenience.

• need to define FOV boundaries for both channels, and split. (define naming convention)

[xiyuyi]

12:40 writing tiffs. (need some time)
12:50 tiff is done. move one.
identify the field of view boundaries for 2 channels. convert for all
1:30 pm identified and converted
4:30 pm did something else now come back

[xiyuyi]

5:32 all PSF labeled. Now thinking about xy range and z range. [tedious step.. need to improve when necessary]

[xiyuyi]

continued worked on exporting identified PSF stacks.

[xiyuyi]

was too busy over the past two months..... now coming back to this project during the part-time.

[xiyuyi]

• go back and get all the calibration distortion fitting scripts, and data checking scripts.
  ------------------peak searching is not perfect, try to optimize a bit.
  ------------------the order of the peaks were messed up. now fixed.

[xiyuyi]

It has been a month again...

automatic PSF crop is here:
H:\DH_localization\Experiments_Phase2_afterSPIE\NW_astig_spetrum_analysis\Sept2019_datacheck.ipynb

[xiyuyi]

identify a paire of beads, 4 PSFs.

beads choice:
Darkred = bead 16
Crimson = bead 25
from the excel list NW_astig_spetrum_data\September2019_CS_3DsSMLM\Sep2019_bead_coordinates.xlsx

choose the one that doesn't have weird cut off background, etc...

location:
H:\DH_localization\Experiments_Phase2_afterSPIE\NW_astig_spetrum_data\September2019_CS_3DsSMLM_tiffs
PSF_Darkred_Order0.tiff
PSF_Darkred_Order1.tiff
PSF_Crimson_Order0.tiff
PSF_Crimson_Order1.tiff

[xiyuyi]

find a group of beads that has a high local density as our demo.

this dataset has a high-density group of beads:
3DMC_Scan (1) right bottom region
3DMC_Scan (6).tif [147, 312], top right, there are two beads one crimson, one darkred
3DMC_Scan (7).tif [156, 310], top right, 3 beads, looks like a mixture
3DMC_Scan (11).tif maybe show a full field of view. frame 328

[xiyuyi]

• generate four testing datasets for this 4-sensing matrix problem

[xiyuyi]

OMG 3 days has passed again...

• organize into 4 test cases.
  all in H:\DH_localization\Experiments_Phase2_afterSPIE\NW_astig_spetrum_analysis\2019_datacheck.ipynb

[xiyuyi]

• write module with 4-A concatenation.

[xiyuyi]

• add DualChannel_diff0CL_diff1_Ticket ticket type
• modify sensing matrix generator(observer) based on the ticket type.