User Manual for Wormfinder Loading images or video sequences
Contents
1. User Manual for Wormfinder Daniel A Wagenaar This user manual describes the Wormfinder Matlab user interface and is meant to be read in conjunction with the paper that describes the algorithm Wormfinder uses D A Wagenaar and W B Kristan 2009 Automated Video Analysis of Animal Movements submitted to Neuroin formatics Loading images or video sequences Click the Load image s button to open the file selection dialog box which can be used to navigate directory trees You can load individual image files in a variety of formats anything supported by Matlab which includes the popular png and jpeg formats or movies in avi format If you select an image file with a number in its name e g img 003 jpg it is assumed to be part of a sequence of images that together make up a video clip and the whole clip is loaded Wormfinder can optionally deinterlace video clips transferred from VHS If the De interlace toggle is active indicated by bold face on the button each image on disk is automatically split into the odd and even frames Setting parameters The text boxes labeled o 0 Thresh and X correspond directly with the parameters described in the paper It is not required to specify oj and explicitly if left blank they default to oj o andA 2 50 You also need to indicate whether your animal is light on a dark background or dark on a light background by selecting eith2. e The Animate button can then be used to display the results for the whole sequence Additionally the navigation buttons see above can be used Correcting problems Problems in individual frames can sometimes be corrected by changing the parameters for that frame only and clicking Detect to enforce them Note that if you click Det all after changing parameters previously detected animal positions will instantly and irretrievably be forgotten and the whole image sequence will be re analyzed with the new parameters 2 If there are objects in particular frames that lead to spurious detections you can drag a rectangle around them and click Exclude to force the program to ignore that area If an object leads to spurious detections in all frames use the Excl all button Saving results Click the Save results button to save the detected animals into a Matlab file A file selection dialog will open which may be used to navigate a directory tree Normally saved files will end in skeleton mat These files may be loaded into Matlab at any later time for further analysis Saved files contain the following variables N is the number of frames Name XXX YY sig_perp sig long lambda thresh scalerect ifnbase vsn Size 100x N 100x N 1xN 1xN 1xN 1xN 1x4 string string Description x coordinates of 100 points on the detected animal in each of N f
3. er the On dark or the On light button The Clean b g toggle selects whether the median of all images in the sequence is subtracted to remove some background clutter as described in the paper The Softmax toggle selects whether a weighted average is used to determine local directionality in that case the orientation x is calculated as l 2 DE zag FG ae 0 and the degree of directionality D x is calculated as D x MEE instead of the calculations shown in the paper Testing detection To test whether the parameters are adequate click the Detect button to find an animal in the currently shown image The results are displayed in the form of a red curve tracing the detected animal s midline The lt lt lt gt gt and gt buttons may be used to navigate an image sequence and frame numbers may also be entered directly in the text box between these buttons to jump to a specific frame The menu button next to the navigation buttons se lects whether to display display the original image Image the original image with median background subtracted W o b g or the extracted direction map Dirmap which shows D x as brightness and x as hue for every pixel in the image Completing detection Once you are satisfied that parameters are reasonable the Det all button can be used to detect animals in all frames of a video clip at onc
4. is way is only possible if the original image s is are still in the same location Contacting the author Please use email for all inquiries daw caltech edu I cannot guarantee support but I do try to respond to all questions Should my email address change in the future the current address may always be found at http www danielwagenaar net
5. rames xxx 1 corresponds to the path of the head xxx end corresponds to the path of the tail y coordinates of 100 points on the detected animal in each of N frames The value of o used in each frame The value of oj used in each frame The value of used in each frame The value of the detection threshold used in each frame The coordinates of any box measured using the Measure button met Xright gt top bottom See below the full pathname of the source of the analyzed data the version identifier of Wormfinder currently 1 0 1 There are a few other variables but those are for internal use It is also possible to save the results as a movie file by clicking Make AVI this is mainly useful for demonstation purposes Including scale information in saved results If you drag a rectangle over an image and click Measure the pixel coordinates of that rect angle will be saved along with the detection results This can be useful to include scale in formation e g if a ruler or grid was included in the image Only the coordinates of the most recently measured rectangle are saved Reloading previous results Should the need arise previously saved results may be reloaded into Wormfinder by clicking the Load results button At that point it is possible to navigate through the detection re sults or to change some parameters and refine the detection Please note that reloading in th
Download Pdf Manuals
Related Search