Stephen Royle

I&#8217;m putting this up here in case it is useful for somebody.
We capture Z-stacks on a Perkin Elmer Spinning Disk microscope system. I wanted to turn each stack into a single image so that we could quickly compare them. This simple macro does the job.
<ol>
<li>We import the images straight from the *.mvd2 library using the wonderful BioFormats import tool. We open all files as composite hyperstacks.</li>
<li>This Macro is then run (works on all of the open images).</li>
<li>It finds the mid-Z point of the stack and sets the brightness/contrast for each channel to Auto.</li>
<li>It then recolours the channels to the right colours (we capture DAPI then GFP then mCherry, but the import colours them red, green and blue, respectively).</li>
<li>Then it makes a z-projection and saves the file in a directory that you specify at the start.</li>
<li>It closes the projection and the z-stack.</li>
</ol>
You can then open up all of the projections, tile them and take a look at what was going on in the experiment.
<pre class="brush: jscript; title: ; notranslate" title="">

setBatchMode(true);
imgArray = newArray(nImages);
dir1 = getDirectory(&quot;Choose Destination Directory &quot;);
for (i=0; i&lt;nImages; i++) {
	selectImage(i+1);
	imgArray&#x5B;i] = getImageID();
	}
for (i=0; i&lt; imgArray.length; i++) {
	selectImage(imgArray&#x5B;i]);
	id = getImageID();
	win = getTitle();
	getDimensions(w, h, c, nFrames, dummy);
	Stack.setSlice(round(nFrames/2));
	run(&quot;Enhance Contrast&quot;, &quot;saturated=0.35&quot;);
	run(&quot;Next Slice &#x5B;&gt;]&quot;);
	run(&quot;Enhance Contrast&quot;, &quot;saturated=0.35&quot;);
	run(&quot;Next Slice &#x5B;&gt;]&quot;);
	run(&quot;Enhance Contrast&quot;, &quot;saturated=0.35&quot;);
	Stack.setChannel(1)
	run(&quot;Blue&quot;);
	Stack.setChannel(2)
	run(&quot;Green&quot;);
	Stack.setChannel(3)
	run(&quot;Red&quot;);
	run(&quot;Z Project...&quot;, &quot;projection=&#x5B;Max Intensity]&quot;);
	saveAs(&quot;TIFF&quot;, dir1+win);
	close();
	selectImage(id);
	close();
	}

</pre>
Sorry for lack of commenting.
&#8212;
Tips from the blog is a <a href="https://quantixed.org/?s=%22tips+from+the+blog%22&amp;submit=Search">series</a> and gets its name from a track from Black Sunday by Cypress Hill.

I'm putting this up here in case it is useful for somebody.

We capture Z-stacks on a Perkin Elmer Spinning Disk microscope system. I
wanted to turn each stack into a single image so that we could quickly
compare them. This simple macro does the job.

1. We import the images straight from the \*.mvd2 library using the
 wonderful BioFormats import tool. We open all files as composite
 hyperstacks.
2. This Macro is then run (works on all of the open images).
3. It finds the mid-Z point of the stack and sets the
 brightness/contrast for each channel to Auto.
4. It then recolours the channels to the right colours (we capture DAPI
 then GFP then mCherry, but the import colours them red, green and
 blue, respectively).
5. Then it makes a z-projection and saves the file in a directory that
 you specify at the start.
6. It closes the projection and the z-stack.

You can then open up all of the projections, tile them and take a look
at what was going on in the experiment.

``` {.brush: .jscript; .title: .; .notranslate title=""}

setBatchMode(true);
imgArray = newArray(nImages);
dir1 = getDirectory("Choose Destination Directory ");
for (i=0; i<nImages; i++) {
 selectImage(i+1);
 imgArray[i] = getImageID();
 }
for (i=0; i< imgArray.length; i++) {
 selectImage(imgArray[i]);
 id = getImageID();
 win = getTitle();
 getDimensions(w, h, c, nFrames, dummy);
 Stack.setSlice(round(nFrames/2));
 run("Enhance Contrast", "saturated=0.35");
 run("Next Slice [>]");
 run("Enhance Contrast", "saturated=0.35");
 run("Next Slice [>]");
 run("Enhance Contrast", "saturated=0.35");
 Stack.setChannel(1)
 run("Blue");
 Stack.setChannel(2)
 run("Green");
 Stack.setChannel(3)
 run("Red");
 run("Z Project...", "projection=[Max Intensity]");
 saveAs("TIFF", dir1+win);
 close();
 selectImage(id);
 close();
 }
```

Sorry for lack of commenting.

---

Tips from the blog is
a [series](https://quantixed.org/?s=%22tips+from+the+blog%22&submit=Search) and
gets its name from a track from Black Sunday by Cypress Hill.

I’m putting this up here in case it is useful for somebody. We capture Z-stacks on a Perkin Elmer Spinning Disk microscope system. I wanted to turn each stack into a single image so that we could quickly compare them. This simple macro does the job. We import the images straight from the *.mvd2 library using the wonderful BioFormats import tool. We open all files as composite hyperstacks.


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