added a figure to show another sequence type (globules without trap)
This sequence `soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0` needs to be processed for the article so I wanted to describe why the preprocessing doesn't give ideal results on it and how to improve it.
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af6fdffdd3
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doc/Makefile
55
doc/Makefile
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@ -9,6 +9,15 @@ lipase.pdf: lipase.tex graphics
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TRAPS_VISIBLE_CONVERTER=convert -contrast-stretch 2%x1% -resize 25%
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GENERATED_GRAPHICS=\
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_nofilter_vis_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_nofilter_vis_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_nofilter_vis_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_327-353_fluo_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_327-353_fluo_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_327-353_fluo_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_420-480_fluo_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_420-480_fluo_000.png \
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graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_420-480_fluo_000.png \
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graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000000_DM300_nofilter_vis_000.png \
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graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000019_DM300_nofilter_vis_000.png \
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graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000039_DM300_nofilter_vis_000.png
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@ -16,17 +25,49 @@ GENERATED_GRAPHICS=\
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.PHONY: graphics
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graphics: $(GENERATED_GRAPHICS)
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graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000000_DM300_nofilter_vis_000.png : $(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_nofilter_vis_000.tif
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$(TRAPS_VISIBLE_CONVERTER) "$<" "$@"
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# creates a rule to list min and max of imanges in an info file for the given sequence
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# creates a rule to convert tif images into png for the given sequence
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# $1 : dir_path : eg soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1
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# $2 : pos_dir : eg Pos0
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# $3 : channel_suffix : eg 420-480_fluo_000
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# $4 : min_value : the maximum pixel value for this channel (eg 631)
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# $5 : max_value : the maximum pixel value for this channel (eg 1441)
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# eg it will create graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_%.png from $(RAW_IMAGES_ROOT_PATH)/soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0/%.tif
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define GENERATE_CHANNEL_IMAGES_CONVERSION_RULE
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graphics/$(subst /,_,$(1))_$(2)_$(3).info:
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convert $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/*$(3).tif -format "%[filename] %[min] %[max]\n" info: 2>/dev/null > "$$@"
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graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000019_DM300_nofilter_vis_000.png : $(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000019_DM300_nofilter_vis_000.tif
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$(TRAPS_VISIBLE_CONVERTER) "$<" "$@"
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graphics/$(subst /,_,$(1))_$(2)_%$(3).png : $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/%$(3).tif graphics/$(subst /,_,$(1))_$(2)_$(3).info
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convert -level $(4)x$(5) -resize 25% "$$<" "$$@"
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endef
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# creates a rule to convert tif images into png for the given sequence
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# $1 : dir_path : eg soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1
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# $2 : pos_dir : eg Pos0
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# eg it will create graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_%.png from $(RAW_IMAGES_ROOT_PATH)/soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0/%.tif
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define GENERATE_TRAP_SEQUENCE_IMAGES_CONVERSION_RULE
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graphics/$(subst /,_,$(1))_$(2)_%.png : $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/%.tif
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$(TRAPS_VISIBLE_CONVERTER) "$$<" "$$@"
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endef
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graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000039_DM300_nofilter_vis_000.png : $(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000039_DM300_nofilter_vis_000.tif
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$(TRAPS_VISIBLE_CONVERTER) "$<" "$@"
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# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_nofilter_vis_000.info
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SEQ_GGHL_RDGL_SGF55_VIS_MIN_VALUE = 13000
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SEQ_GGHL_RDGL_SGF55_VIS_MAX_VALUE = 65535 # yes, the images are saturated!
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$(eval $(call GENERATE_CHANNEL_IMAGES_CONVERSION_RULE,soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1,Pos0,nofilter_vis_000,$(SEQ_GGHL_RDGL_SGF55_VIS_MIN_VALUE),$(SEQ_GGHL_RDGL_SGF55_VIS_MAX_VALUE)))
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# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_327-353_fluo_000.info
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SEQ_GGHL_RDGL_SGF55_F340_MIN_VALUE = 631
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SEQ_GGHL_RDGL_SGF55_F340_MAX_VALUE = 1441
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$(eval $(call GENERATE_CHANNEL_IMAGES_CONVERSION_RULE,soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1,Pos0,327-353_fluo_000,$(SEQ_GGHL_RDGL_SGF55_F340_MIN_VALUE),$(SEQ_GGHL_RDGL_SGF55_F340_MAX_VALUE)))
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# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_420-480_fluo_000.info
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SEQ_GGHL_RDGL_SGF55_F450_MIN_VALUE = 700
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SEQ_GGHL_RDGL_SGF55_F450_MAX_VALUE = 1800
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$(eval $(call GENERATE_CHANNEL_IMAGES_CONVERSION_RULE,soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1,Pos0,420-480_fluo_000,$(SEQ_GGHL_RDGL_SGF55_F450_MIN_VALUE),$(SEQ_GGHL_RDGL_SGF55_F450_MAX_VALUE)))
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$(eval $(call GENERATE_TRAP_SEQUENCE_IMAGES_CONVERSION_RULE,res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1,Pos0))
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.PHONY: clean
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clean:
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rm -f $(GENERATED_GRAPHICS)
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rm -f $(GENERATED_GRAPHICS) graphics/*.info
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rm -f lipase.pdf lipase.aux lipase.fls lipase.log lipase.fdb_latexmk lipase.dvi;
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@ -258,6 +258,77 @@
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\label{fig:trap_sequence1}
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\end{figure}
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\begin{figure}
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\centering
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_nofilter_vis_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 0}
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%\label{fig:1}
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\end{subfigure}
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~
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_nofilter_vis_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 19}
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%\label{fig:1}
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\end{subfigure}
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~
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_nofilter_vis_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 39}
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%\label{fig:1}
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\end{subfigure}
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\\
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\centering
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_327-353_fluo_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 0, 327nm - 353nm}
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%\label{fig:1}
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\end{subfigure}
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~
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_327-353_fluo_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 19, 327nm - 353nm}
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%\label{fig:1}
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\end{subfigure}
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~
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_327-353_fluo_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 39, 327nm - 353nm}
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%\label{fig:1}
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\end{subfigure}
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\\
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\centering
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_420-480_fluo_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 0, 420nm - 480nm}
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%\label{fig:1}
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\end{subfigure}
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~
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_420-480_fluo_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 19, 420nm - 480nm}
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%\label{fig:1}
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\end{subfigure}
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~
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\begin{subfigure}[b]{0.3\textwidth}
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\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_420-480_fluo_000.png}
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%\includegraphics[width=\textwidth]{1.png}
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\caption{Frame 39, 420nm - 480nm}
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%\label{fig:1}
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\end{subfigure}
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\caption{Example of trap sequence (\texttt{soleil2016/GGHL\_rDGL\_SGF55\_lambda\_Em\_cinsuite\_1/Pos0})}
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\label{fig:sequence_gghl1}
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\end{figure}
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\subsection{computing the circularness image}
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\label{sec:circularness}
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