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| -rw-r--r-- | README.markdown | 40 |
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diff --git a/README.markdown b/README.markdown index c49fa40..30ee934 100644 --- a/README.markdown +++ b/README.markdown @@ -58,7 +58,7 @@ scripts directory. 1. Cropping and Extracting Cell Images 2. Deriving Cell Backgrounds 3. Generating Cell Masks -4. Filtering Masks +4. Filtering Cell Masks 5. Fly Tracking ### Step 1: Cropping and Extracting Cell Images ### @@ -93,3 +93,41 @@ This will take some time, and require a lot of CPU and disk space. ### Step 2: Deriving Cell Backgrounds ### +The second step of the process is deriving the background image from the video. +By doing this, we can subtract the background from the current frame to generate +the mask. When subtracted the parts left over are the fly, while things in the +background won't show up. + + process-video-beta -v First10MinGroup1.avi -l Group1First10MinCropFile -n 1 -t First10MinSet -d data/ -2 + +This will derive the backgrounds for all of the Cells in the video seperately. +After this tool is done running, it will output the Background.png into the mask +folder. $data-root/$settype$setnumber/Background.png, for example it might be in +data/First10MinSet2/Background.png. + +Verify this image. Sometimes when the flies do not move the background might +include the fly! If there are any left of flie parts, use GIMP to airbrush over +that section with an appropriate color (guess what the background would be +"close" too). + +### Step 3: Generating Cell Masks ### + +The third step of the process is generating the Masks from the background and +the cropped images. + + process-video-beta -v First10MinGroup1.avi -l Group1First10MinCropFile -n 1 -t First10MinSet -d data/ -3 + +This step will output the masks in $data-root/$settype$setnumber/Masks/ + +### Step 4: Filtering Cell Masks ### + +The fourth step is the filtering step. It's important because it makes sure the +masks do not have stray objects in them (which will mess up the final tracking +sequence) + + + process-video-beta -v First10MinGroup1.avi -l Group1First10MinCropFile -n 1 -t First10MinSet -d data/ -4 + +The filtered masks are in $data-root/$settype$setnumber/Filtered/final/ + + |