Cory Quammen

CISMM Microscope Simulator 1.3.1 Released

Cory Quammen — Thu, 17 Sep 2009 18:34:34 +0000

Today I released the CISMM Microscope Simulator 1.3.1 software available here. This version adds a Point Set model that enables you to specify an arbitrary number of single fluorophore locations.

How to fix Preview PDF font display problem in Mac OS X Leopard

Cory Quammen — Mon, 11 May 2009 01:54:15 +0000

If PDF documents show up funny within Preview, particularly if the fonts appear wrong, there is a simple fix. Open up a Terminal window and type

killall -u ATSServer

Restart Preview and the problem should be fixed.

Producing video files that will play in PowerPoint in Windows from still frames

Cory Quammen — Sun, 22 Mar 2009 18:20:45 +0000

Often, you’ll have a sequence of image files from which you’d like to make a movie that plays in PowerPoint for presentations. The best way I’ve found to do this is to create Windows Media files. Here is the recipe I’ve found that works well using Windows XP. You’ll need to download ImageJ and Windows Media Encoder. Your mileage may vary.

Open ImageJ (version 1.41 or above is recommended). Load the sequence (File->Import->Image Sequence…). The length of the videos you can create is limited with this method, but it works well enough for videos that are under 10 seconds long. You should be able to encode longer still frame sequences by opening the image sequence as a virtual stack.
Crop the video so that the width and height of the videos are even numbers. Otherwise, Windows Media Encoder will save that the AVI is not valid.
Save the image sequence as an AVI file (File->Save As->AVI…). Choose JPEG as the compression method and set the quality to 100. Set the frame rate to something reasonable (e.g. 10, 15, 30 fps).
Open Windows Media Encoder. In the New Session wizard, choose “Convert a file”. Set the source file to the AVI you exported from ImageJ. Set the output file to the name you want. Click next. Choose the type of content distribution you are targeting. For playback in PowerPoint, choose “File download (computer playback)”. Click next. This will result in the highest quality video. Under encoding options, choose something suitable. I choose “High definition quality video (5 Mbps VBR)”. Click next. Name the video and click next. Under the “Settings Review” panel, uncheck the “Begin converting when I click Finish” checkbox and click Finish.
Before doing anything else, we’ll change the size of the output video. Click on the “Properties” button in the toolbar at the top of the application window. Click on the “Video Size” tab. Under the “Crop” settings, choose method “Custom”. Under the “Resize” settings, choose “No resizing” unless you want the video to be resized. When finished, click “Apply”.
Finally, click the “Start Encoding” button in the toolbar. You’ll see a preview of your video as the encoding proceeds.

That’s it. Now test out your video in PowerPoint and make sure it plays in presentation mode.

An Introduction to Durham, NC

Cory Quammen — Sun, 22 Feb 2009 22:27:00 +0000

CL: How to compute the average of a column of numbers in a text file

Cory Quammen — Sun, 01 Feb 2009 16:06:06 +0000

Awk makes computing the average of a column of numbers in a text file very easy. Here’s the command for computing the average of the 5th column in a text file:

cat my_file.txt | awk '{sum=sum+$5}END{print sum/NR}'

The $5 means the 5th column and the NR means the number of entries (rows) in the column.

CL: How to extract columns from a text file

Cory Quammen — Sun, 01 Feb 2009 15:57:14 +0000

The ‘cut’ utility on Linux/Unix is useful for selecting columns from a delimited text file. It’s basic usage is

cat my_file.txt | cut -d ' ' -f 2

This will select the second column from a space-delimited file. The -d option specifies the delimiter (default is tab) and the -f option specifies a comma-separated list of columns that you want to select from the file.

How to reset your iPod Mini

Cory Quammen — Mon, 12 Jan 2009 16:29:11 +0000

My iPod Mini freezes about once a month. Resetting it is fairly simple by following the directions on this Apple web page.

Clarity 1.0 Deconvolution Library Released

Cory Quammen — Sun, 14 Dec 2008 22:51:21 +0000

I have released version 1.0 of the Clarity deconvolution library. Clarity is an open-source C/C++ library implementing many of the common deconvolution algorithms used in fluorescence microscopy. It is designed specifically for processing 3D images generated from optical sectioning microscopy. Clarity uses multithreaded algorithms to make full use of all the cores on modern multi-core computer systems. For even greater performance, the deconvolution algorithms can optionally run on commodity graphics processing units that feature hundreds of computing cores. Support for acceleration on graphics processing units is currently available on NVIDIA graphics cards.

CL: How to remove CVS directories from a project directory

Cory Quammen — Sat, 13 Dec 2008 01:11:28 +0000

To remove CVS files from a module you have checked out from a CVS repository, you can use a simple one-line command:

find -type d -wholename '*CVS' | xargs /bin/rm -rf

Execute this from the root of the CVS module that you checked out and want to clean up.

Cumin-Scented Stir-Fried Beef with Celery

Cory Quammen — Tue, 25 Nov 2008 02:05:44 +0000

Here’s a simple but delicious beef stir fry recipe from Epicurious.com.

http://www.epicurious.com/recipes/food/views/Cumin-Scented-Stir-Fried-Beef-with-Celery-350561