20150603T044839: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 JOIN #fiji-devel 20150603T044850: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 PRIVMSG #fiji-devel :hello? 20150603T044850: qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130: hello? 20150603T045150: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 PRIVMSG #fiji-devel :I am trying to write a script in Fiji to run the TrackMate plugin on all the files in a directory. Right now I am having trouble actually replicating the TrackMate settings that I use in the gui in the script. My first issue is that I get spots of various sizes, instead spots of uniform size that I acquire in the gui 20150603T045150: qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130: I am trying to write a script in Fiji to run the TrackMate plugin on all the files in a directory. Right now I am having trouble actually replicating the TrackMate settings that I use in the gui in the script. My first issue is that I get spots of various sizes, instead spots of uniform size that I acquire in the gui 20150603T045250: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 PRIVMSG #fiji-devel :All I want to do is write a script that does the following (I will describe the settings chosen as if I am using the gui) 20150603T045250: qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130: All I want to do is write a script that does the following (I will describe the settings chosen as if I am using the gui) 20150603T045739: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 PRIVMSG #fiji-devel :Pixel width: 1392, height: 1040, time interval: 12 frame. Next. LoG detector. Next. Estimated blob diameter: 25.0 pixel, threshold 0.5, use median filtering, do sub-pixel localization. Next. Next. Next. Hyperstack displayer. Next. Uniform Color. Next. Simple LAP Tracker. Next. Linking max distance: 40 pixel, gap closing max distance: 15.0 pixel, gap-closing frame gap: 3. Next. Capture Overlay, execute. Export tracks to XM 20150603T045739: qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130: Pixel width: 1392, height: 1040, time interval: 12 frame. Next. LoG detector. Next. Estimated blob diameter: 25.0 pixel, threshold 0.5, use median filtering, do sub-pixel localization. Next. Next. Next. Hyperstack displayer. Next. Uniform Color. Next. Simple LAP Tracker. Next. Linking max distance: 40 pixel, gap closing max distance: 15.0 pixel, gap-closing frame gap: 3. Next. Capture Overlay, execute. Export tracks to XM 20150603T052858: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 PRIVMSG #fiji-devel :#---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ 20150603T052858: qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130: #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ 20150603T055834: *: <== :qwebirc48520!32cdfd82@gateway/web/freenode/ip.50.205.253.130 QUIT :Ping timeout: 246 seconds 20150603T113522: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu JOIN #fiji-devel 20150603T122727: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu QUIT :Quit: Leaving. 20150603T123959: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu JOIN #fiji-devel 20150603T144505: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu QUIT :Quit: Leaving. 20150603T145220: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu JOIN #fiji-devel 20150603T161415: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu QUIT :Quit: Leaving. 20150603T165858: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu JOIN #fiji-devel 20150603T193219: *: <== :hinerm!~Adium@dyn-144-92-48-243.microscopy.wisc.edu QUIT :Quit: Leaving. 20150603T210316: *: <== :tdsmith!~tim@tds.xyz QUIT :Ping timeout: 265 seconds 20150603T210525: *: <== :tdsmith!~tim@tds.xyz JOIN #fiji-devel