User:Bohao Liu/Notebook/Research/2014/04/30

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(Image Analysisp)
Current revision (14:30, 30 April 2014) (view source)
(HOG Experiments : wild - type controls and Image Analysis Parameters)
 
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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====
Line 34: Line 43:
**<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
 
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run("Set Measurements...", "area mean centroid redirect=None decimal=3");
 
-
 
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//Asks for directory
 
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dir = getDirectory("Choose a Directory");
 
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folderList = getFileList(dir);
 
-
 
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for (i = 0; i < folderList.length; i++)
 
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{
 
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if (endsWith(folderList[i], "/"))
 
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{
 
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wellList = getFileList(dir+folderList[i]);
 
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for (j = 0; j < wellList.length; j++)
 
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{
 
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fileList = getFileList(dir+folderList[i]+wellList[j]);
 
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//Now starts actual analysis
 
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filename = dir+folderList[i]+wellList[j]+fileList[0];
 
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//Opens image sequence, c1 is mCherry
 
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run("Image Sequence...", "open=filename starting=1 increment=1 scale =100 file=[] or=c1. sort");
 
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run("Subtract Background...", "rolling=50 stack");
 
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setAutoThreshold("Otsu dark");
 
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run("Threshold...");
 
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run("Convert to Mask", "  black");
 
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run("Erode","stack");
 
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run("Despeckle","stack");
 
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run("Analyze Particles...", "size=25-100 circularity=0.50-1.00 show=Nothing add stack");
 
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close();
 
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run("Image Sequence...", "open=filename starting=1 increment=1 scale =100 file=[] or=c2. sort");
 
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run("Subtract Background...", "rolling=50 stack");
 
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roiManager("Measure");
 
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//CHANGE ME******************
 
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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";
 
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saveAs("Results", saveName);
 
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roiManager("Reset");
 
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run("Clear Results");
 
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close();
 
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}
 
-
 
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}
 
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}
 
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</code>
 
-
 

Current revision

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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




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