Electronic Imaging for Microscopy
Client: U.S. Air Force Research Laboratory - Wright-Patterson AFB Summary: This is a cross-disciplinary effort directed towards modernizing the digital microscopy facilities in RX by developing advanced tools for segmentation of image data collected. The effort involves a team consisting of Signal Processing specialists, software development specialists, and Materials Science specialists. The ultimate goal is to develop Graphical User Interface (GUI)-based software that implements modern segmentation algorithms to be used on serial section image data of the microstructures of materials.Code Availability:
All code will be available from the BlueQuartz Public The BlueQuartz Software Gitorious server.Tier 1 Data Sets
| Data Set Designation | Desciption | Zip Format | MXA Format | Example Image |
|---|---|---|---|---|
| MNML-3 | NanoEnergetic Material with 3 Phases | MNML-3_769_780.zip | MNML-3_769_780.mxa.zip | NanoEnergetic Material MNML-3 |
| NanoSilicate | NanoComposite Material | Nano-Silicate.zip | Nano-Silicate.mxa.zip | NanoComposite Material |
| Rene-88 Dual Heat Treat | This is a data set acquired on the AFRL FIB by Mike Uchic and Jeremiah MacSleyne on February 16, 2006. It consists of 188 slices with a slice thickness of 25 nm. | Rene88DT.zip | Rene88DT.mxa.zip | Rene-88 Dual Heat Treat |
| Rene-88 -2 | This is a data set acquired on the AFRL FIB by Mike Uchic and Jeremiah MacSleyne on May 11, 2005. It consists of 54 slices with a slice thickness of 50 nm. | Rene88DT-2.zip | Rene88DT-2.mxa.zip | Rene-88 Dual Heat Treat |
| IN100 | This data set was obtained using the WPAFB FIB by Mike Uchic and is generally known as "THE" IN100 data set. It was acquired on June 25th, 2004 (and following days) and consists of 170 slices each of 4 tilts in the FIB Instrument. | IN100.zip | IN100.mxa.zip | IN100 Ni Alloy |
Phantom Segmentations
| Data Set Designation | Desciption | Zip Format | MXA Format |
|---|---|---|---|
| NiCrAl 25 keV Simulation | The data set consists of 257 slices of 513x513 pixel TIFF images. Each image represents a 15 nm thick slice, and the pixel dimensions are also 15x15 nm. Microscope parameter is 25 keV | NiCrAl-simulated.tar.gz | None Available |
| NiCrAl 1 keV Simulation | The data set consists of 257 slices of 513x513 pixel TIFF images. Each image represents a 15 nm thick slice, and the pixel dimensions are also 15x15 nm. Microscope parameter is 1 keV | NiCrAl-simulated-b.tar.gz | None Available |
| NiCrAl 1 keV Simulation Cylindrical Precipitates | The data set consists of 257 slices of 513x513 pixel TIFF images. Each image represents a 15 nm thick slice, and the pixel dimensions are also 15x15 nm. Microscope parameter is 1 keV | NiCrAl-simulated-c.tar.gz | None Available |
Ground Truth Segmentations
| Data Set Designation | Desciption | Zip Format | MXA Format |
|---|---|---|---|
| Rene88DT-GT | This data set consists of 50 conscutive slices from the Rene88DT data set. The original images were 979x813x188, and a sub-volume of 256x256x50 was selected at the location (70,160,0) (with the origin in the lower left corner of the image. | Rene88DT-GT.tar.gz | None Available |
| Nanosilicate Tomography | This data set consists of 46 slices from a NanoSilicate Organic Compound. Each image is 834 W x 729 H pixels. The images have been segmented into two classes. | Nanosilicate_Tomography_GT.zip | None Available |
Misc. Data Sets
| Data Set Designation | Desciption | Zip Format | MXA Format |
|---|---|---|---|
| MNML-5 | NanoEnergetic Material with 2 Phases | MNML-5_610_640.zip | MNML-5_610_640.mxa.zip |
| Martensite Steel | Optical Micrographs from a Martensitic Steel Sample. Courtesy of US Navy Research Labs and Dr. Rowenhorst | Martensite.zip | None Available |
Electronic Imaging for Microscopy Documents and Guides:
The following documents are being constructed as part of the contract. All are under construction and should be considered as draft.Software Coding Style - Guidelines for writing more portable software codes using CMake and other accepted software development practices. HTML, PDF
Doxygen Guide - A quick tutorial on the use of the Doxygen commenting system for source codes HTML, PDF
Source Code Management - Recommendations for the use of a Source Code Management system when developing computer software. HTML, PDF
Instructions that show how to setup a new Ubuntu 10.04 LTS server. How to install the Gitorious server side program that will allow others to access your git repositories. The installation instructions also include how to install Gitorious on OS X 10.6 (Client) and some basic instructions on how to use Gitorious. HTML, PDF