Curvelet-Based Alignment Analysis (CurveAlign and CurvePrep)
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20130227_xlwrite
CircStat2012a
ExperimentalScripts
FIRE
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TumorTrace Add short README for TumorTrace Jun 4, 2012
batch_input_csvbound CurveAlign Test Cases May 29, 2013
batch_input_fire_nobound
batch_input_fire_tiffbound
batch_input_nobound
ctFIRE
deploy
xlscol
.gitignore
BDcreationHE.m
BDcreation_reg.m
CAV2_20130206.zip
CAroi.m
CTrec.m
CurveAlign Users Manual.docx
CurveAlign.m
CurvePrep.m
FindConnectedPts.m
FindOutlineSlope.m
GetFirstNeighbor.m
GetSegPixels.m
LICENSE-third-party.txt Add license description for xlwrite Mar 24, 2017
LICENSE.txt
Original_curvelets_user_guide.pdf
README.txt Add references to Curvelet Transform and FIRE Aug 1, 2018
addCurvelabAddressFn.m
all_images.lnk
batch_curveAlign.m Fix add path deploy bug Nov 22, 2013
callctFIRE.m
checkBndryFiles.m Checking in two missing files Jun 11, 2014
checkCAoutput.m
checkCTFireFiles.m to check the .mat file of a stack Oct 30, 2015
curvTrain.m This is a workable CurveAlign Beta version 3.0 primarily based on Jer… Jun 20, 2014
drawCurvs.m
drawMap.m
fixAngle.m
getBoundary.m
getCT.m
getCTroi.m
getFIRE.m
getFileName.m
getTifBoundary.m
goCAK.m processImageCK is the CK version of "processImage" Oct 20, 2015
group6.m
makeStats.m
makeStatsO.m
makeStatsOROI.m
mccgoCAK.m
newCurv.m
param_reg1_0530.m
parametersCAKpc.txt
processImage.m
processImageCK.m
processROI.m
svmAnalysis.m Changed KM figure limits, colors and line specs Jan 14, 2014
writeAllHistData.m

README.txt

This software package includes two tools, i.e. CurveAlign(1-3) and CT-FIRE(4-5) for collagen fiber quantification. CurveAlign is a curvelet transform (CT)-based quantitative tool for interpreting the regional interaction between collagen and tumors by assessment of up to ~thirty fiber features, including angle, alignment, and density. CT-FIRE analyzes individual fiber metrics such as length, width, angle, and curvature. The individual fibers extracted by CT-FIRE can be imported into the CurveAlign as one of the two fiber analyse modes. The approach of CT-FIRE is described in (4), which combines the advantages of the fast discrete curvelet transform(6) for denoising images, enhancement of the fiber edge features, and the fiber extraction (FIRE) algorithm (5) for extracting individual fibers.  For now, CurveAlign should be used for bulk assessment of collagen features including angles/density and CT-FIRE for individual fiber quantification.

CurveAlign and CT-FIRE are licensed under the 2-Clause BSD license as described LICENSE.txt, except for some third-party code whose licenses are described in LICENSE-third-party.txt. One third-party code, CurveLab 2.1.2 MATLAB package for curvelet transform, can only be downloaded from http://www.curvelet.org/software.html. To run CurveAlign or CT-FIRE, the CurveLab needs to be downloaded and added to the Matlab searching path.

Link to CurveAlign: http://loci.wisc.edu/software/curvealign
Link to CT-FIRE:    http://loci.wisc.edu/software/ctfire

References:

CurveAlign: 
1. Schneider, C.A., Pehlke, C.A., Tilbury, K., Sullivan, R., Eliceiri, K.W., and Keely, P.J. (2013). Quantitative Approaches for Studying the Role of Collagen in Breast Cancer Invasion and Progression. In Second Harmonic Generation Imaging, F.S. Pavone, and P.J. Campagnola, eds. (New York: CRC Press), p. 373.


2. Bredfeldt, J.S., Liu, Y., Conklin, M.W., Keely, P.J., Mackie, T.R., and Eliceiri, K.W. (2014). Automated quantification of aligned collagen for human breast carcinoma prognosis. J Pathol Inform 5.


3. Liu, Y., Keikhosravi, A., Mehta, G.S., Drifka, C.R., and Eliceiri, K.W. (accepted). Methods for quantifying fibrillar collagen alignment. In Fibrosis: Methods and Protocols, L. Rittié, ed. (New York: Springer), p.


CT-FIRE
4. Bredfeldt, J.S., Liu, Y., Pehlke, C.A., Conklin, M.W., Szulczewski, J.M., Inman, D.R., Keely, P.J., Nowak, R.D., Mackie, T.R., and Eliceiri, K.W. (2014). Computational segmentation of collagen fibers from second-harmonic generation images of breast cancer. Journal of Biomedical Optics 19, 016007–016007.

5. Stein, A. M., Vader, D. A., Jawerth, L. M., Weitz, D. A. & Sander, L. M. An algorithm for extracting the network geometry of three-dimensional collagen gels. J. Microsc. 232, 463–475 (2008).

Fast Discrete Curvelet Transform:
6. Candes, E., Demanet, L., Donoho, D. & Ying, L. Fast discrete curvelet transforms. Multiscale Model. Simul. 5, 861–899 (2006).