Movie Color Visualization

Mon 04 February 2013 by Dr. Dirk Colbry

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As part of my work with the Campus Champion Fellowship I have been asked to look into methods for displaying color for an entire movie similar to the following:

ColourSpectrograms
MovieBarCode

I tried installing the ColourSpectrograms java software but had some trouble. So, I tried implimenting an algorithm myself. The following are my results so far:

Average Image|HSV Video Colormap|Average Bar|Link to video

---|---|---|---

|||Video Tutorial - GlobusOnline.org

|||Video Tutorial - HPCCUSB

|||No video available on-line

Currently the algorithm is very slow and written in Python. The colors are based on the HSV colorspace which can be visually understood using the following image:

Note: Image obtained from http://www.mathworks.com/help/images/converting-color-data-between-color-spaces.htmlI use the V (value) channel to determine if a color is black then I use the H (Hue) channel to histogram the remaining colors for each image and display the histogram linerally by color. I think this is working but it doesn't really show the variations in color that you see with the MovieBarCode. Most notably is that since I do not use the S (saturation) channel there is no white or offwhite colors in the graph. I think this is a good start but will have to talk though the best way to proceed with the rest of the team.

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Speeding up Scientific Imaging Workflows- Design of Automated Image Annotation Tool

Wed 16 January 2013 by Dr. Dirk Colbry

Blog post edited by Anonymous - "Migrated to Confluence 4.0"

Below are the slides that I presented at the User Centered Computer Vision workshop.

Abstract:
Low cost digital cameras have transformed the process of collecting data. Researchers can now generate massive datasets and analyze the images later, either manually or …

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CI-Days presentation - From Images to Data- Scaling and Streamlining Research Workflows

Fri 02 November 2012 by Dr. Dirk Colbry

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Below are the slides from my MSU CI-Days presentation.

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2012-10-26 Colbry CI-Days Talk.pdf

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ffmpeg to select video sequences

Thu 01 November 2012 by Dr. Dirk Colbry

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ffmpeg can be used to crop the start and end times of a video sequece. Use the following command to read though the ffmpeg help message in the terminal window:

       man ffmpeg

Use arrow …

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Image Phenomics- The Development of an Image Grammar for High-Throughput Phenotyping Using Biological Images

Mon 01 October 2012 by Dr. Dirk Colbry

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I was excited to give a talk as part of the BEACON seminar series. Our research group has been working on this topic for a while and it is exciting to get all of the ideas down into one clear …

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Research Software Design Tradeoffs

Thu 02 August 2012 by Dr. Dirk Colbry

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After the successes (and setbacks) of our five summer undergraduate research assistants, we finally have a useable ChamView prototype that is based on my concept of an image grammar. My work over the last week or so has been to …

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Summer Undergraduate Research Students

Tue 31 July 2012 by Dr. Dirk Colbry

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I had a wonderful opportunity this summer to work with five undergraduate students on my research. The students were part of a 10 week research program and worked on different components of the ChamView Project. This was the largest group …

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Drosophila Tour

Fri 15 June 2012 by Dr. Dirk Colbry

Blog post edited by Anonymous - "Migrated to Confluence 4.0"We had the opportunity last week to stop by the Dworkin lab for a quick tour.Dr. Ian Dworkin (link toDworkinlab) is doing someinteresting work studying evolution and drosophila wings (fruit flies). He hadrows of cages, each filled with different …

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Microscope Demonstration

Wed 06 June 2012 by Dr. Dirk Colbry

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Our research team had an opportunity to see a demonstration of an Olympus two-photon microscope .
This impressive piece of hardware can take focused depth images into a sample.These types of scopes are used specifically with biological samples that canbe …

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Image Stitching

Tue 29 May 2012 by Dr. Dirk Colbry

Blog post edited by Anonymous - "Migrated to Confluence 4.0"I have a video stitching program that I wrote in MATLAB to combine twooverlapping videos into one (See figure below):Combining two overlapping videos into one image is an important step in ourscientific workflow for studying chameleons. Without image stitching …

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