Commit 162808fb authored by Chris Evenhuis's avatar Chris Evenhuis
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Added results file

parent 33065cf9
analysis-plots/B-tubulin-r2-circ.png

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analysis-plots/B-tubulin-r2-circ.png

14.6 KB | W: | H:

analysis-plots/B-tubulin-r2-circ.png
analysis-plots/B-tubulin-r2-circ.png
analysis-plots/B-tubulin-r2-circ.png
analysis-plots/B-tubulin-r2-circ.png
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date,org,treat,rep,time,psi,psi_05,psi_95,mu,mu_05,mu_95,alpha,alpha_05,alpha_95
22,B-tubulin,control,2,24,0.2146568000666046,0.09470775520952596,0.3738563568128989,1.049196697906249,0.4371918793863856,1.831921990042692,2.1806523313946533,0.8551277965693186,4.2494974177188025
22,B-tubulin,control,2,48,0.07848485612548645,0.026440421109927042,0.15128038663960214,1.4701615670644066,0.5905249924507936,2.8437715551079887,2.0216176692196264,0.7936462011778878,3.9790945573635934
22,B-tubulin,0.5xMIC,2,24,0.985959182246495,0.9404278533414212,0.9999892103583736,1.7512862202859023,1.3916793065745192,2.133577530235759,4.409756789832672,2.2252656636189654,7.5717008412109505
22,B-tubulin,0.5xMIC,2,48,0.9833249804711156,0.9339060982084304,0.9999940107773778,1.7398330058074891,1.4473193619919953,2.0434659324207014,4.848763901872553,2.556932341519273,8.233056722792398
22,H99WT,control,2,24,0.09439215720406732,0.03180862855936612,0.17781387310664476,1.2242624172414494,0.4689614791671943,2.35024347029942,2.0354175107249444,0.7999210581039904,4.084120346566958
22,H99WT,control,2,48,0.005276933932296818,6.103694734453864e-07,0.023274111002031857,3.8242044508101998,0.9975212151364148,8.877430459629354,1.9670556986602827,0.7056067555409367,3.9567739695623474
22,H99WT,0.5xMIC,2,24,0.10056151505014843,0.03485641230248657,0.1913030132984324,1.2084254367330372,0.4306342251352913,2.297685924553299,2.063918020667605,0.8115854480628246,4.066984259098864
22,H99WT,0.5xMIC,2,48,0.00443877060539191,6.678469687683018e-07,0.01957047112416765,3.827027394966189,0.9798333149755204,9.04043143230235,1.967352928714052,0.7081143615220814,3.8510521287414963
29,H99WT,control,2,24,0.011644611772833834,1.8411003069340735e-07,0.0504688827432668,3.7892890806616912,0.981935102442016,9.025926149164967,1.9692411064850368,0.7370049184688692,3.930117096424663
29,H99WT,control,2,48,0.008807458926398006,8.637625893191396e-06,0.038506542161411285,3.809086101690811,1.0254070614225936,8.910792777561824,1.9572719726157768,0.6920809315519268,3.886182952473337
29,H99WT,1xMIC,2,24,0.9858607952386896,0.9386301515797084,0.9999981534981413,1.315662717909684,1.0454035093828624,1.6185044738031058,4.6305094112696885,2.343070603033828,7.967798988085638
29,H99WT,1xMIC,2,48,0.9589283421155588,0.8302586752175982,0.999996790562508,2.1516988379195103,1.2705049216173765,3.1928857324633997,2.8971852501579685,1.265951364549933,5.391623257504784
29,H99WT,control,1,24,0.06550809191561728,0.01648307828325709,0.13270453321199158,1.4902484436609076,0.5194915318639997,3.032795653998326,1.9779678192702983,0.6840246676248425,3.8021799839761887
29,H99WT,control,1,48,0.005089036719205556,5.498145167609227e-07,0.022154615247847738,3.784719562522692,1.0545618458382275,9.158868949568122,1.9654686210959889,0.6908029107225215,3.8926795781833694
29,H99WT,1xMIC,1,24,0.9644761849961558,0.8743778220943753,0.9999917518128272,0.6644824092688898,0.531706241203131,0.8068481877191791,3.822943135800753,1.90570039538865,6.589475282796199
29,H99WT,1xMIC,1,48,0.9796063919997012,0.92251021613896,0.9999866331175646,1.1239205248051842,0.8864651724031555,1.3692505681979463,4.109925375026801,2.038046545831691,7.226120110937513
29,H99S,control,1,24,0.11491272153152955,0.04943928912658693,0.20212776175287106,0.9775890716417184,0.4338515799181133,1.7031621890575137,2.1784925649196984,0.8542990570322784,4.338857295000193
29,H99S,control,1,48,0.004301073367153579,1.62099523606486e-06,0.01826977140873512,3.831750524989456,0.9422760824366904,8.929141720989143,1.966940687844538,0.7183569719400063,3.923631088546614
29,H99S,1xMIC,1,24,0.978654553665968,0.9130448471666416,0.9999874043174818,0.9293113100503476,0.7192717125326848,1.157687079987055,4.102023176458279,2.0033043359912384,7.197209064798461
29,H99S,1xMIC,1,48,0.9375693512504736,0.7900229571268536,0.9999831185499068,1.5858575105220702,1.0445563167633192,2.2582820269026884,2.6904868178507666,1.179903350589686,5.026967480224148
29,Yox1KO,control,1,24,0.12652978810716942,0.053345445884694837,0.2256214581981473,0.9441789535311608,0.4026047860473173,1.7179600448529406,2.1683369443749534,0.776666590875722,4.2769842495190336
29,Yox1KO,control,1,48,0.004453459971361194,4.335903608390316e-07,0.02003659838876326,3.8145096168478054,0.9980182437368008,9.103561902558726,1.9634747257986649,0.7441838486444085,3.8879330571289215
29,Yox1KO,1xMIC,1,24,0.96905699632546,0.8819685397851635,0.9999972467399708,1.0273432710924604,0.7945528987989809,1.298191524912708,3.718414068922242,1.852063044241289,6.644646898149081
29,Yox1KO,1xMIC,1,48,0.984482700644927,0.9353170716854876,0.9999936493004958,1.7665067879154397,1.4106932821469726,2.1579483422897128,4.726955215350637,2.3852899235207103,8.070608930425461
29,Yox1KO,control,2,24,0.13297552506643426,0.05748928482365207,0.2379198696975255,0.8971540523036485,0.4084072803716233,1.5727723809531913,2.1895564406372343,0.8602470289667649,4.2645568032203975
29,Yox1KO,control,2,48,0.01095944833344899,0.0004082579432454511,0.031628294944272266,2.9393427154748166,0.844478484720445,6.6050922389208475,1.9168139895907657,0.7389202413773075,3.799960545035714
29,Yox1KO,1xMIC,2,24,0.9765255717005284,0.907986738275948,0.999998992188304,1.29604563104705,0.962070016409015,1.6496686278202128,3.9277489158652337,1.8244486429459883,6.8157084897058535
29,Yox1KO,1xMIC,2,48,0.9620195711307772,0.860162631995254,0.9999959362464472,1.6272263505982087,1.17412343259786,2.1571814707706247,3.3597201520737827,1.5012978881125143,6.067583991653862
22,B-tubulin,control,1,24,0.4157290903343819,0.2119181359617348,0.659123112045949,0.937689466516238,0.4667423679204591,1.5207595086268508,2.269459873288074,0.986588887569468,4.370688882260391
22,B-tubulin,control,1,48,0.244193301269352,0.12285353607812233,0.4122273882902969,0.8388862421240733,0.4063147471579461,1.4007457058121364,2.278500664408176,0.9160331920398388,4.411103763870409
22,B-tubulin,0.5xMIC,1,24,0.9895185185987504,0.9563831484302368,0.9999996158866892,1.6950074595935882,1.3659035649056959,2.073576813499488,4.1567841027417565,2.081339597498157,6.810169894494917
22,B-tubulin,0.5xMIC,1,48,0.9873983065265516,0.9502324631392948,0.9999924210653766,1.35786770730936,1.121683901168084,1.6209340458434824,4.743377589422262,2.399247503587825,7.96764986923502
22,H99WT,control,1,24,0.41537114706138967,0.222412553240825,0.6714820440125291,0.9282082277562529,0.4698811333846202,1.567542651664458,2.2436026353892347,0.918939077265633,4.264235717048352
22,H99WT,control,1,48,0.24363467733415756,0.12321738176445092,0.41639953458936724,0.8343677254363373,0.402938374100279,1.408053166802238,2.2810820971731824,0.9188186318860786,4.48986247345021
22,H99WT,0.5xMIC,1,24,0.989033123002718,0.9561616357998721,0.9999986314434057,1.701502840264602,1.3668833254412713,2.0625397608419314,4.124857835698593,2.0385031967953955,6.844257761464438
22,H99WT,0.5xMIC,1,48,0.9874943073961036,0.9489243084296282,0.9999983405807199,1.35663017399784,1.1202656582897699,1.6220335272365154,4.731952099496752,2.339360866969849,7.947576526004317
......@@ -317,9 +317,9 @@ def ridge_detection_for_string(imp):
#impt.show()
ridge_opt1="line_width=3 low_contrast=160 high_contrast=200 "
ridge_opt2="minimum_line_length=20 maximum=20000 correct_position stack "
ridge_opt3="estimate_width extend_line add_to_manager method_for_overlap_resolution=SLOPE"
ridge_opt1="line_width=3 low_contrast=160 high_contrast=200 "
ridge_opt2="minimum_line_length=20 maximum=20000 correct_position stack "
ridge_opt3="estimate_width extend_line add_to_manager method_for_overlap_resolution=SLOPE"
#'sigma=1.37 lower_threshold=5.61 upper_threshold=10.88 '
ridge_opt="{} {}".format(ridge_opt1,ridge_opt2)
IJ.run(impt,"Ridge Detection",ridge_opt1+ridge_opt2+ridge_opt3)
......@@ -408,9 +408,9 @@ def analyse_gfp_roi(imp_i, roi, ch=2):
return roi_ret
if( __name__=='__builtin__'):
igfp=1
# prompt for file
if( True ):
if( False ):
[dir_n, nd2_n, map_n, roi_n] = select_file()
prefs = Prefs()
load_rois( roi_n, path=dir_n)
......@@ -419,6 +419,7 @@ if( __name__=='__builtin__'):
date=int(dir_n.split(prefs.separator)[-3][-2:])
# set the GFP channel
if( date==22): igfp=0+1
if( date==29): igfp=2+1
......@@ -460,6 +461,7 @@ if( __name__=='__builtin__'):
roim = RoiManager.getInstance()
rois = roim.getRoisAsArray()
from ij.process import ImageStatistics
from ij.measure import ResultsTable, Measurements
......@@ -497,7 +499,7 @@ if( __name__=='__builtin__'):
if( -50<abs(ir-0) ):
print(ir,iframe,ic)
string_rois=[]
string_rois = analyse_gfp_roi(imp,roic,ch=igfp)
string_rois = analyse_gfp_roi(imp,roic,ch=igfp) # detect the string
for s_roi in string_rois:
print("add")
s_roi.setPosition(igfp,s_roi.getZPosition(),iframe)
......
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