Curvelet-Based Alignment Analysis (CurveAlign and CurvePrep)
Matlab
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20130227_xlwrite "xlwrite" Copyright (c) 2013, Alec de Zegher Jul 30, 2014
CircStat2012a Latest Trentham batch analysis May 29, 2013
ExperimentalScripts Rearranging and adding comments May 29, 2013
FIRE fix syntax errors Oct 20, 2015
LocalStash Added comment Feb 7, 2013
TumorTrace Add short README for TumorTrace Jun 4, 2012
batch_input_csvbound CurveAlign Test Cases May 29, 2013
batch_input_fire_nobound GUI updates Apr 8, 2014
batch_input_fire_tiffbound GUI updates Apr 8, 2014
batch_input_nobound
ctFIRE Update description of the main program of CT-FIRE Mar 30, 2017
deploy V2.2 Release Jun 3, 2013
xlscol the third party code for converting numbers to Excel column letters Nov 7, 2014
.gitignore Latest Trentham batch analysis May 29, 2013
BDcreationHE.m use newest segmention function for boundary creation Nov 15, 2016
BDcreation_reg.m
CAV2_20130206.zip Added comment Feb 7, 2013
CAroi.m
CTrec.m
CurveAlign Users Manual.docx
CurveAlign.m close the last overlay and heatmap after full image analysis or ROI a… Sep 1, 2017
CurvePrep.m Latest version Jun 4, 2012
FindConnectedPts.m
FindOutlineSlope.m add for debug the error of wrong relative angle calculation Nov 6, 2015
GetFirstNeighbor.m
GetSegPixels.m Update for JPI analysis Sep 18, 2013
LICENSE-third-party.txt Add license description for xlwrite Mar 24, 2017
LICENSE.txt Add license for both CT-FIRE and CurveAlign. Need to add a descriptio… Feb 23, 2017
Original_curvelets_user_guide.pdf
README.txt Update readme file Mar 23, 2017
addCurvelabAddressFn.m CurveAlign - need to add CA_Boundary folder to the image being opened Feb 8, 2016
all_images.lnk Latest Trentham batch analysis May 29, 2013
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 Check in "checkACoutput" and add stack check for both checkCAoutput a… Jan 30, 2017
checkCTFireFiles.m
curvTrain.m This is a workable CurveAlign Beta version 3.0 primarily based on Jer… Jun 20, 2014
drawCurvs.m make the color consistent with Version 2.3 Sep 23, 2015
drawMap.m format Aug 10, 2016
fixAngle.m Latest version Jun 4, 2012
getBoundary.m output features and feature name in csv file. debugged the CT- no bou… Jun 13, 2014
getCT.m
getCTroi.m accept the update of the nearest fibers and box size parameters from … Sep 12, 2016
getFIRE.m Specify the option for middle point estimation Feb 8, 2017
getFileName.m Comment update May 30, 2013
getTifBoundary.m set the properties of the points out of the interested regions to NaN… Apr 26, 2016
goCAK.m processImageCK is the CK version of "processImage" Oct 20, 2015
group6.m Comment update May 30, 2013
makeStats.m donot calculate overall alignment when boundary is used Sep 25, 2015
makeStatsO.m add the calculation of the total pixels within the near boundary region Apr 15, 2016
makeStatsOROI.m make statistics for the angle in ROI post-processing Dec 21, 2015
mccgoCAK.m command to compile goCAK and goCTFK Oct 20, 2015
newCurv.m resume the adaptive edge buffer that depends on the image size in Cur… Oct 5, 2016
param_reg1_0530.m common parameters used by ctFIRE_1.m Dec 6, 2012
parametersCAKpc.txt add parameters file for testing Oct 20, 2015
processImage.m Fix the colormap of heatmap automatically scaled issue, the color pix… Aug 30, 2017
processImageCK.m Fix the colormap of heatmap automatically scaled issue, the color pix… Aug 30, 2017
processROI.m Fix the colormap of heatmap automatically scaled issue, the color pix… Aug 30, 2017
svmAnalysis.m Changed KM figure limits, colors and line specs Jan 14, 2014
writeAllHistData.m Updates for today Oct 7, 2013

README.txt

This software package includes two tools, i.e. CurveAlign and CT-FIRE for collagen fiber quantification. CurveAlign is a 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. 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: 
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.


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.


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
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.