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clairelbromley / ZebrafishKymographing

Various software tools written for analysis of lumen opening and membrane retraction in zebrafish.
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Striping in CZI-generated kymographs #107

Closed clairelbromley closed 7 years ago

clairelbromley commented 7 years ago

image

Presence of striping artefacts in kymographs generated from blebbistatin data in cziFig

clairelbromley commented 7 years ago

metadata.umperpixel 0.237219 metadata.xoffset 0.000000 metadata.yoffset 0.000000 metadata.cutFrame 1.000000 metadata.cutMetadata.startPositionX 442.000000 metadata.cutMetadata.stopPositionX 444.000000 metadata.cutMetadata.startPositionY 309.000000 metadata.cutMetadata.stopPositionY 345.000000 metadata.cutMetadata.time 0.000000 metadata.cutTheta 1.515298 metadata.embryoNumber 1 metadata.acquisitionDate 260417 metadata.cutNumber 1.000000 metadata.kym_region.xcut 442.000000 444.000000 metadata.kym_region.ycut 309.000000 345.000000 metadata.kym_region.kym_startx 444.169174 443.935339 443.701504 443.467670 443.233835 443.000000 442.766165 442.532330 442.298496 442.064661 441.830826 metadata.kym_region.kym_starty 348.045135 343.836108 339.627081 335.418054 331.209027 327.000000 322.790973 318.581946 314.372919 310.163892 305.954865 metadata.kym_region.pos_along_cut -0.723477 0.276523 1.276523 2.276523 3.276523 4.276523 5.276523 6.276523 7.276523 8.276523 9.276523 metadata.kym_region.fraction_along_cut -0.084587 0.032330 0.149248 0.266165 0.383083 0.500000 0.616917 0.733835 0.850752 0.967670 1.084587 metadata.kym_region.distance_from_edge 0.723477 0.276523 1.276523 2.276523 3.276523 4.276523 3.276523 2.276523 1.276523 0.276523 0.723477 metadata.kym_region.deltay -4.160251 metadata.kym_region.deltax 74.884526 metadata.kym_region.kym_endx 519.053701 518.819866 518.586031 518.352196 518.118361 517.884526 517.650692 517.416857 517.183022 516.949187 516.715352 metadata.kym_region.kym_endy 343.884883 339.675856 335.466829 331.257802 327.048775 322.839749 318.630722 314.421695 310.212668 306.003641 301.794614 metadata.kym_region.boundingBox_LTRB 440.000000 300.000000 521.000000 350.000000 metadata.kym_region.cropped_xcut 2.000000 4.000000 metadata.kym_region.cropped_ycut 9.000000 45.000000 metadata.kym_region.cropped_kym_startx 4.169174 3.935339 3.701504 3.467670 3.233835 3.000000 2.766165 2.532330 2.298496 2.064661 1.830826 metadata.kym_region.cropped_kym_endx 79.053701 78.819866 78.586031 78.352196 78.118361 77.884526 77.650692 77.416857 77.183022 76.949187 76.715352 metadata.kym_region.cropped_kym_starty 48.045135 43.836108 39.627081 35.418054 31.209027 27.000000 22.790973 18.581946 14.372919 10.163892 5.954865 metadata.kym_region.cropped_kym_endy 43.884883 39.675856 35.466829 31.257802 27.048775 22.839749 18.630722 14.421695 10.212668 6.003641 1.794614 metadata.isCropped 1 metadata.acqMetadata.cycleTime 1.483700 userOptions.forcedSpeedRange -1.500000 1.500000 userOptions.forcedPositionRange -5.000000 20.000000 userOptions.fixedNumberOrFixedSpacing 1 userOptions.kymSpacingUm 1.000000 userOptions.number_kym 10.000000 userOptions.kymDownOrUp 1.000000 userOptions.timeBeforeCut 0.000000 userOptions.timeAfterCut 369.441300 userOptions.quantAnalysisTime 29.674152 userOptions.kym_width 1.000000 userOptions.kym_length 75.000000 userOptions.scatterComparisonOnly 0 userOptions.loadPreprocessedImages 0 userOptions.scale_bar_length 20.000000 userOptions.outputFolder /Users/clairebromley/Desktop/untitled folder 3 userOptions.saveFirstFrameFigure 1 userOptions.firstFigureTitleAppend
userOptions.saveCutPositioningFigs 1 userOptions.removeCutFrames auto userOptions.figHandle 1.000000 userOptions.savePreprocessed 1 userOptions.avgOrMax 1.000000 userOptions.erosionDilation 1 userOptions.medianFiltKernelSize 1.000000 userOptions.preProcess 1 userOptions.showKymographOverlapOverlay 1 userOptions.calculateExpSpeeds 0 userOptions.basalMembraneKym 0 userOptions.usePreviouslySavedBasalPos 0 userOptions.manualOrAutoApicalSurfaceFinder manual userOptions.usePreviouslySavedApicalSurfacePos 0 userOptions.flip90DegForShortCuts 0 userOptions.lumenOpening 0 userOptions.speedInUmPerMinute 0 userOptions.crossSize 7.000000

clairelbromley commented 7 years ago

screen shot 2017-07-04 at 22 15 01

dougkelly88 commented 7 years ago

Compare nearest, bilinear and bicubic interp methods: image image image

As of 63ce06d6bdd210106a4ca02f4e60f2b4d53c4531, use bilinear interpolation by default when generating line profiles.