September 2025 M T W T F S S « Aug 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Categories
- AP patterning (13)
- Blog (1)
- Chromatin (88)
- Conference Notes (72)
- Fly Work (54)
- General STORM (25)
- Genomics (134)
- Journal Club (22)
- Lab Meeting (66)
- Microscopy (79)
- Notes (1)
- probe and plasmid building (58)
- Project Meeting (3)
- Protocols (13)
- Research Planning (74)
- Seminars (21)
- Shadow Enhancers (59)
- snail patterning (40)
- Software Development (5)
- Summaries (1,412)
- Teaching (9)
- Transcription Modeling (40)
- Uncategorized (10)
- Web development (19)
Links
Tags
analysis cell culture cell labeling chromatin cloning coding communication confocal data analysis embryo collection embryo labeling figures fly work genomics hb image analysis image processing images in situs Library2 literature making antibodies matlab-storm meetings modeling MP12 mRNA counting Ph planning presentation probe making project 2 project2 result results sectioning section staining shadow enhancers sna snail staining STORM STORM analysis troubleshooting writing-
GitHub Projects
Protected: project 2: update 08/12/14
Posted in Genomics
Comments Off on Protected: project 2: update 08/12/14
Monday 08/11/14
9:30 am – 5:10 pm, 10:00 pm – 12:30 am
Meetings
- group meeting (notes)
- journal club (notes)
Project 2
- see notes
STORM
- finish staining chr-L4 A01, A02, A01 to A03.
- setting up to image A01 to A03
- make new Glox solution
- staining failed. Check probes by Gel. I guess plate-columns don’t work so well…
Coding
- modified ChromatinCropper to have option to use conventional images taken immideately prior to storm data to drift correct the conventional images in multi-color taken at the very beginning of the run.
- tested function and incorporated into main GUI
- currently on CCupdate branch. Ready to merge back into master.
Probe diagnostics
- Gel order: gel 1: 1,2, 9,10, 17,18, P3:1,2, gel 2: F1-F7, E9-E6
- these actually look reasonable,
- though maybe the concentration of the L4 probes is extremely low since these samples are taken from purified final probe (15 uL) and the L2 and L3 samples are equally bright but taken from diluted RT reactions (~800 uL). Should nanodrop.
Ph Project
- working on supplement on interpreting cluster sizes and counts
- explaining STORM vector data
- explaining geometric distributed data.
Posted in Summaries
Comments Off on Monday 08/11/14
Journal Club 08/11/14
Presented by Shu
Mapping Brain with Diffuse Optics
- Optical methods as alternative to MRI or PET (which are not electronic embedded device compatable, e.g. parkinson’s deep brain stimulator or pacemakers or young children).
- Compare IR specta at 750 and 860, distinguish oxygenated vs. deoxygenated hemoglobin (Onaral lab, Drexel)
- measure backscattered light in these wavelengths
- penetration depth of up to 1 cm into brain regions.
- limitations
- tradeoff in head coverage vs. spatial resolution
- sensitive to haemodynamics in superficial tissue (e.g. scalp / non-brain activity)
- no structural information (shape of head, where photons came from).
setup details
- usse fMRI to generate head model. (get head shape).
- 96 sources and 92 detectors -> 1200 usuable source detector pairs.
comparison to fMRI
- see pretty good correlation with fMRI and known brain region – function correlations.
- e.g. audio processing, visual processing etc.
- can correlate activity from different brain regions to pull out connectivity.
- analyzed in resting state networks — just getting correlated connectivity, not necessarily progressive transforms of thought.
- some subjects show better and worse correlation to fMRI
Sunday 08/10/14
10:30 am – 3:00 pm, 4:00 pm – 6:00 pm, 9:00 pm – 12:00 am
cell prep
- prepping cells for hybe
Probe making
- eluted probes on plate-columns
- currently transferred to 8-well strips
New hybe
- testing new probes
- chromatin Lib 4
- A01,
- A02,
- A01 to A3
data processing
- running daoSTORM analysis on last week’s multi-color data
project 2
- see notes
Posted in Summaries
Comments Off on Sunday 08/10/14
Friday 08/08/14
10:00 am – 5:50 pm, 8:15 pm – 12:15 am
Project 2
- see posts
Chromatin STORM
- both new black region stains failed – very weak spots.
- L3D10-D12
- L3D11-D12
- not sure why, previously got great stains with D11 and D12
Cell prep
- fixed more cells.
- rest of prehybe prep still needs to be done
Ordering
- ordered new probe making supplies
- ordered more coverglass
- ordered more insect Media (SFX)
Discussion with XZ
- deadline for Burroughs-Wellcome approaching
- I’ll take K99 winter app deadline, SW will take fall.
Posted in Summaries
Comments Off on Friday 08/08/14