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Prairie scope analysis

Acquisition and analysis workflow for Prairie two-photon scope

PUT THIS TOGETHER WITH CURRENT NOTES SITTING ON DESKTOP OF COMPUTER

Operator’s Manual pdf

Scope ID is 4647

Original Quote pdf

Current workflow

To Do (understanding how to acquire good images)

To Do (Pre-process raw data)

To Do (Efficiency)

To Do (Video)

To Do (Igor)

To Do (the fucking analysis)

Ideas

Converting .h264 to .mp4

#!/bin/bash

#INPUT="$1"

mkdir mp4

for file in *.h264 ; do
	filename="${file%.*}"
	echo $filename
	ffmpeg -r 30 -i "$file" -vcodec copy "mp4/$file.mp4"
	sleep 3
done

Raspberry

Raspberry ip is 10.16.81.61

Raspberry To Do

Prairie View blog with updates and release notes

https://pvupdate.blogspot.com/

Fiji plugin for prairie

See Prairie View blog side-bar

https://www.dropbox.com/s/in593hvhc2v3dwj/Prairie_Reader.zip?dl=0

Prairie emission filters

Scope ID is 4647, use to search email for long threads with technicians ending around 11/11/16 - 12/5/16

This is from the original scope quote (20150528), assuming it is what we have?

Dual emission filters (et525/70m-2p and et595/50m-2p) and t565lpxr dichroic beam splitter for simultaneous viewing and acquisition from both detectors

See Thermo Fischer Fluorescence SpectraViewer for (Texas Red emission profile)[https://www.thermofisher.com/us/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html]

With red filter centered at 595 nm we are collecting ~ 50% of Texas Red emission. But the band is 50m which should do the job? But may not be enough?

Sutter red filter

This is from email to Zeng You 20150416, did he replace this?

The red filter in front of the PMT is from Chroma and is a HQ 610/75m

(HQ 610/75m)[https://www.chroma.com/products/parts/hq610-75m]

Synch code to robertcudmore.org

Treadmill is synching code to robertcudmore.org with unison

Install unison with

sudo apt-get install unison

Save this into /home/pi/.unison/treadmill.prf

# Unison preferences file
root = /home/pi/Sites/treadmill
root = ssh://robertcu@robertcudmore.org/raspberry/Sites/treadmill

#ignore = Path */raw/*

ignore = Name *.pyc
ignore = Name .git*
ignore = Name .*
ignore = Name .DS_Store
ignore = Name *.DS_Store
ignore = Name *.shtml
ignore = Name *.htaccess

# Be fast even on Windows
#fastcheck = yes

servercmd=/home1/robertcu/unison
Tags: analysis

©2017. Robert Cudmore.