imageplot_documentation.rtf

{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf600
{\fonttbl\f0\fswiss\fcharset0 Helvetica;\f1\fmodern\fcharset0 Courier;}
{\colortbl;\red255\green255\blue255;\red0\green0\blue0;\red249\green249\blue249;}
{\*\expandedcolortbl;;\cssrgb\c0\c0\c0;\cssrgb\c98039\c98039\c98039;}
\margl1440\margr1440\vieww12500\viewh13260\viewkind0
\deftab720
\pard\pardeftab720\partightenfactor0

\f0\fs24 \cf0 #this is not an R script, it is a text file written in that style to facilitate understanding\
\
#This method will utilize software called ImageJ, currently deployed through Fiji\
\
1. Secure images in a single location, in this case /Users/danielfaltesek/desktop/kinkade\
\
\
2. Two Methods\
A. Run qtip on said images\
This will produce a CSV which does two things:\
i. produces a reference file of measurements\
ii. produces a concise list of file names \
\
B. Import the image folder (in this case \'93pictures\'94) into ImageJ\
file>import>image sequence\
In the dialog, import as a \'93virtual stack\'94\
Measurements can be created by\
Analyze>Set Measurements\
In the dialog, set all desired measures \
Process>Batch>Measure\
Save the results (produces an old excel file, .xls)\
\
3. Modify the CSV, either use excel and delete the SECOND row or use R, \
Method for R: my data<-mydata[-c(2,),]\
OR use the dplyr method \
paint<-slice(painting, 2:7)\
\
4. Image J - run macro, Image Plot\
\
5. Both selections should be to open; since you have used QTip, your data structure will be easily integrated into the program\
\
6. Run plugin; this is where things get annoying. Your DATA NEEDS TO BE IN A TXT (tab delimited)\
A. Excel is a fine can opener\
B. If you want to use R, which at this point, why not? \
\pard\pardeftab720\sl320\partightenfactor0

\f1\fs28 \cf2 \cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 \strokec2 write.table(mydata, "mydata.txt", sep=\'93\\t\'94, row.names=FALSE)
\f0\fs24 \cf0 \cb1 \kerning1\expnd0\expndtw0 \outl0\strokewidth0 \
\pard\pardeftab720\partightenfactor0
\cf0 \
run macro -> select file -> open the txt -> select options\
\
7. View basic image plot - the issue then becomes, how do we interpret the information that we have found? \
\
8. Check the data dictionary \
\
9. Color Thresholding and Particle Detection are Easily Possible\
\
Cool Outputs\
stk>make montage\
3dproject\
\
Radials Orthagonals\
\
5D VIEWER\
plugins>analyze>cell counter\
\
Color Inspector 3d\
\
MONTAGE IS UP AND RUNNING\
TAB DELIMTED TEXT IS KEY\
\
Image Montage\
\
BEST METHOD\
Call the files directly in the sheet\
\
1. Make measurement\
2. Add levels \
3. BE SURE TO SAVE AS TXT (tab delimited text)\
\
L-measure can do neurons (what data structure does that look like?\
VAIS aligns stacks of images\
\
\
Image>type\
process - watershed OR another threshold method\
analysis>analyze particles \
\
}