Difference between revisions of "User:Bohao Liu/Notebook/Research/2014/04/30"

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(Image Analysisp)
(fix raw html notebook nav)
 
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|-
 
|-
 
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
 
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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|style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
 
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| colspan="2"|
 
| colspan="2"|
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====Settings====
 
====Settings====
 
*30 second half-period
 
*30 second half-period
*5 second imaging = 6 images per cycle
+
*6 second imaging = 6 images per cycle
 
*5 minute total time = 5 complete periods
 
*5 minute total time = 5 complete periods
 +
*30 minutes in between for a total of 5 sets
 +
 +
*1 hour rest after this set of 5
 +
 +
*30 second half-period
 +
*6 second imaging = 6 images per cycle
 +
*20 minute total time = 20 complete periods
  
 
*ND=2
 
*ND=2
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*GFP = 200 mS exposure
 
*GFP = 200 mS exposure
 
*DIC
 
*DIC
 +
 +
  
 
====Image Analysisp====
 
====Image Analysisp====
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**<code>for /l %x in (1,1,5) do MD well%x</code>
 
**<code>for /l %x in (1,1,5) do MD well%x</code>
 
**<code>for /l %x in (1,1,5) do MOVE col*t*xy%xc*.tif well%x</code>
 
**<code>for /l %x in (1,1,5) do MOVE col*t*xy%xc*.tif well%x</code>
 
 
<code>//Sets Measurements
 
run("Set Measurements...", "area mean centroid redirect=None decimal=3");
 
 
//Asks for directory
 
dir = getDirectory("Choose a Directory");
 
folderList = getFileList(dir);
 
 
for (i = 0; i < folderList.length; i++)
 
{
 
if (endsWith(folderList[i], "/"))
 
{
 
wellList = getFileList(dir+folderList[i]);
 
for (j = 0; j < wellList.length; j++)
 
{
 
fileList = getFileList(dir+folderList[i]+wellList[j]);
 
 
//Now starts actual analysis
 
filename = dir+folderList[i]+wellList[j]+fileList[0];
 
 
//Opens image sequence, c1 is mCherry
 
run("Image Sequence...", "open=filename starting=1 increment=1 scale =100 file=[] or=c1. sort");
 
run("Subtract Background...", "rolling=50 stack");
 
setAutoThreshold("Otsu dark");
 
run("Threshold...");
 
run("Convert to Mask", "  black");
 
run("Erode","stack");
 
run("Despeckle","stack");
 
run("Analyze Particles...", "size=25-100 circularity=0.50-1.00 show=Nothing add stack");
 
close();
 
run("Image Sequence...", "open=filename starting=1 increment=1 scale =100 file=[] or=c2. sort");
 
run("Subtract Background...", "rolling=50 stack");
 
roiManager("Measure");
 
 
//CHANGE ME******************
 
saveName = "C:\Users\NIKON\Documents\Bohao\HOG\Results"+substring(folderList[i],0,lengthOf(folderList[i])-1)+substring(wellList[j],0,lengthOf(wellList[j])-1)+"nuc.txt";
 
saveAs("Results", saveName);
 
roiManager("Reset");
 
run("Clear Results");
 
close();
 
}
 
 
}
 
}
 
</code>
 
 
  
  

Latest revision as of 23:56, 26 September 2017

Owwnotebook icon.png Project name Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

HOG Experiments : wild - type controls and Image Analysis Parameters

Objective

  • Make sure I can do HOG experiments again
  • Confirm Wild-type values and also expand the frequencies tested
  • Confirm the protocol: specifically that waiting 30 minutes between each set of oscillations is enough to ensure that the cells return to normal
  • See if the cells are growing

Experiment

  • Cells OD @ 10 = .453
  • Started flow at 10:45 am
  • Started experiment at 11:15 am

Settings

  • 30 second half-period
  • 6 second imaging = 6 images per cycle
  • 5 minute total time = 5 complete periods
  • 30 minutes in between for a total of 5 sets
  • 1 hour rest after this set of 5
  • 30 second half-period
  • 6 second imaging = 6 images per cycle
  • 20 minute total time = 20 complete periods
  • ND=2
  • mCherry = 200 mS exposure
  • GFP = 200 mS exposure
  • DIC


Image Analysisp

  • for windows sorting :
    • for /l %x in (1,1,5) do MD well%x
    • for /l %x in (1,1,5) do MOVE col*t*xy%xc*.tif well%x