Fwd: ImageJ behavioral analyses: can it do the following?
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Fwd: ImageJ behavioral analyses: can it do the following?
 
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Hello ImageJ Community:
Can ImageJ do the things listed below? If "yes" where in ImageJ are those functions located? Thank you. 1. Put time stamp on a digital video (can it do this in fast forward speed and keep track of correct time)? 2. Keep track of length (hence distances, I had the presence of mind to place a scale at the beginning of each "take") throughout the videos. 3. Digitally mark individuals (maximum number of organisms on screen is 6, typically it is 4) so that the program (not the observer) can aautomatically follow movements and, hence, give a crude estimate of real distances and, with time also captured, speed, etc. can be calculated 4. As the digital video is rolling, the observer annotates the database (as the program is hopefully doing 1-3) including what are the organisms doing (e.g. mating, preening, etc.) and allows more than one activity per individual to be marked at the same time. 5. Anything else you think I may have forgotten. If you have any specific and constructive suggestions, please kindly send me a message off the list. [hidden email] Gratefully, Jorge P.S. Apologies for potential duplicate emails. Jorge A. Santiago-Blay, PhD blaypublishers.com 1. Positive experiences for authors of papers published in *LEB* http://blaypublishers.com/testimonials/ 2. Free examples of papers published in *LEB*: http://blaypublishers.com/category/previous-issues/. 3. *Guidelines for Authors* and page charges of *LEB*: http://blaypublishers.com/archives/ *.* 4. Want to subscribe to *LEB*? http://blaypublishers.com/subscriptions/ http://blayjorge.wordpress.com/ http://paleobiology.si.edu/staff/individuals/santiagoblay.cfm -- Jorge A. Santiago-Blay, PhD blaypublishers.com 1. Positive experiences for authors of papers published in *LEB* http://blaypublishers.com/testimonials/ 2. Free examples of papers published in *LEB*: http://blaypublishers.com/category/previous-issues/. 3. *Guidelines for Authors* and page charges of *LEB*: http://blaypublishers.com/archives/ *.* 4. Want to subscribe to *LEB*? http://blaypublishers.com/subscriptions/ http://blayjorge.wordpress.com/ http://paleobiology.si.edu/staff/individuals/santiagoblay.cfm -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Jorge,
1. Under Image > Stacks > Label you can add a time stamp to your time series. 2. Use the 'Straight line' ROI to mark your scale bar. Go to Analyze > Set Scale and the distance of your line is given in pixels. You have to add the correct length under 'Known distance' + Units. 3. This depends on many factors of your images like quality, angle, background etc but sounds like a job for a tracking plugin. If you go to the ImageJ plugins site and search for tracking you will find several plugins. Fiji has under the menu Plugins an item 'Tracking' or do a google search as there might be plugins out there on personal web sites. 4. Not sure what you mean by "annotates the database". If you want to annotate the images you could for example use something like the cell counter plugin (http://rsbweb.nih.gov/ij/plugins/cell-counter.html). Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging Facility Centre for Core Biotechnology Services University of Leicester http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif ImageJ workshops 17 -18 December: http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif/workshops/imagej-workshops-17-and-18-December-2015 -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jorge A. Santiago-Blay Sent: 24 October 2015 22:52 To: [hidden email] Subject: Fwd: ImageJ behavioral analyses: can it do the following? Hello ImageJ Community: Can ImageJ do the things listed below? If "yes" where in ImageJ are those functions located? Thank you. 1. Put time stamp on a digital video (can it do this in fast forward speed and keep track of correct time)? 2. Keep track of length (hence distances, I had the presence of mind to place a scale at the beginning of each "take") throughout the videos. 3. Digitally mark individuals (maximum number of organisms on screen is 6, typically it is 4) so that the program (not the observer) can aautomatically follow movements and, hence, give a crude estimate of real distances and, with time also captured, speed, etc. can be calculated 4. As the digital video is rolling, the observer annotates the database (as the program is hopefully doing 1-3) including what are the organisms doing (e.g. mating, preening, etc.) and allows more than one activity per individual to be marked at the same time. 5. Anything else you think I may have forgotten. If you have any specific and constructive suggestions, please kindly send me a message off the list. [hidden email] Gratefully, Jorge P.S. Apologies for potential duplicate emails. Jorge A. Santiago-Blay, PhD blaypublishers.com 1. Positive experiences for authors of papers published in *LEB* http://blaypublishers.com/testimonials/ 2. Free examples of papers published in *LEB*: http://blaypublishers.com/category/previous-issues/. 3. *Guidelines for Authors* and page charges of *LEB*: http://blaypublishers.com/archives/ *.* 4. Want to subscribe to *LEB*? http://blaypublishers.com/subscriptions/ http://blayjorge.wordpress.com/ http://paleobiology.si.edu/staff/individuals/santiagoblay.cfm -- Jorge A. Santiago-Blay, PhD blaypublishers.com 1. Positive experiences for authors of papers published in *LEB* http://blaypublishers.com/testimonials/ 2. Free examples of papers published in *LEB*: http://blaypublishers.com/category/previous-issues/. 3. *Guidelines for Authors* and page charges of *LEB*: http://blaypublishers.com/archives/ *.* 4. Want to subscribe to *LEB*? http://blaypublishers.com/subscriptions/ http://blayjorge.wordpress.com/ http://paleobiology.si.edu/staff/individuals/santiagoblay.cfm -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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