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+ | ====== Striper ====== | ||
+ | |||
+ | STRIPER you to strip your filaments out of the micrograph automatically. | ||
+ | |||
+ | {{: | ||
+ | |||
+ | |||
+ | ===== Overview ===== | ||
+ | {{:: | ||
+ | |||
+ | ===== Installation ===== | ||
+ | |||
+ | Activate the " | ||
+ | add [[https:// | ||
+ | | ||
+ | ===== Get your data into ImageJ ==== | ||
+ | === Load the raw data === | ||
+ | - File -> Import -> Image Sequence | ||
+ | - Select the folder of your images | ||
+ | - Type the file ending into "File name contains:" | ||
+ | - Check "Use virtual stack" | ||
+ | - Press OK Now you have read in your data as an image stack. | ||
+ | |||
+ | === Reduce the size === | ||
+ | |||
+ | For the sake of memory consumption and speed your should reduce the size / image depth of your image data. | ||
+ | - Image -> Adjust -> Size | ||
+ | - Set the width to 1024. The height is calculated automatically. | ||
+ | - Press OK. | ||
+ | - Image -> Type -> 8 Bit Wait until the processing is finished. | ||
+ | |||
+ | === Save the file for later use === | ||
+ | File -> Save As -> Tiff... | ||
+ | |||
+ | ===== Parameters ===== | ||
+ | |||
+ | ==== Detection ==== | ||
+ | |||
+ | As there is no easy way to guess the lower and upper threshold, it is recommended to use the detection assistant (File -> Detection assistant). | ||
+ | |||
+ | **Filament width:** | ||
+ | |||
+ | The width of your filaments in pixel. | ||
+ | |||
+ | **Mask width (Advanced option):** | ||
+ | |||
+ | As the response along the filament randomly fluctuates and sometimes disappear, it is important to average along the filament. | ||
+ | |||
+ | **Lower threshold: | ||
+ | |||
+ | Filter responses lower than that value will be considered as background and filament tracing stops here.Higher values lead to more segmented lines, as low contrast regions of a filament will be considered as background the line is splitted at this position. | ||
+ | |||
+ | **Upper threshold: | ||
+ | |||
+ | Filter responens higher than that will be considered as valid filament starting point.With higher values the contrast of the filaments have to higher be to be picked. | ||
+ | |||
+ | **Equalize: | ||
+ | |||
+ | After enhancement of the filaments, all images are adjusted that filamants have a more similar absolute response. Especially when the image contains high contrast contaminations, | ||
+ | |||
+ | ==== Filtering ==== | ||
+ | **Min number of boxes:** | ||
+ | |||
+ | The minimum number of boxes that have to be placed per line. | ||
+ | |||
+ | ---- | ||
+ | |||
+ | === Response filter === | ||
+ | |||
+ | **Sigma min. response:** | ||
+ | |||
+ | The mean response M and the standard deviation S are estimated over all lines per image. If a line has a signficant number of line points __below__ the threshold T = M-F*S it is considered as false-positiv (background) and is removed, whereas F is value to specifiy.By default, this filter is deactivated (set to 0). A resonable value lies typically between 2 - 3. | ||
+ | |||
+ | **Sigma max. response:** | ||
+ | |||
+ | The mean response M and the standard deviation S are estimated over all lines per image. If a line has a signficant number of line points __above__ the threshold T = M+F*S it is considered as false-positiv (ice, | ||
+ | |||
+ | **Sensitivity: | ||
+ | |||
+ | Threshold value for minimum straightness. Line segments (see window size) with a straightness below that threshold will be removed and the line is splitted. Higher values means that the filament have to be more straight, where 1 means a perfect straight line. | ||
+ | |||
+ | ---- | ||
+ | |||
+ | === Straightness filter === | ||
+ | **Min. straightness: | ||
+ | |||
+ | Threshold value for minimum straightness. Line segments (see window size) with a straightness below that threshold will be removed and the line is splitted. Higher values means that the filament have to be more straight, where 1 means a perfect straight line. | ||
+ | |||
+ | **Window size:** | ||
+ | |||
+ | The number of line points which are used to estimate the straightness. Larger values lead to more robustness against noisebut decrease to ability to detect small curves. | ||
+ | |||
+ | |||
+ | ---- | ||
+ | |||
+ | ** Allowed box overlap: ** | ||
+ | |||
+ | Relative amount to what extend two boxes auf different filaments are allowed to overlap. The default value 0.5 which is the maximum value that ensures that a box contains only one filament | ||
+ | |||
+ | |||
+ | |||
+ | ==== General ==== | ||
+ | |||
+ | ===== Step-by-Step Tutorial ===== | ||
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