striper

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striper [2020/03/02 11:45] (current)
twagner created
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 +====== Striper ======
 +
 +STRIPER you to strip your filaments out of the micrograph automatically.
 +
 +{{:​actin.png?​direct&​300 |}}{{ :​actin_processed.png?​direct&​300 |}} 
 +
 +
 +===== Overview =====
 +{{::​screen_shot_2017-12-08_at_12.43.57.png?​direct&​200 |}} Striper is the filament particle picking procedure used in our lab.
 +
 +===== Installation =====
 +
 +Activate the "​biomedgroup"​ update site and 
 +add [[https://​imagej.net/​Following_an_update_site|a new update site]]:
 +     ​http://​sites.imagej.net/​Mpi-do-stripper/​
 +===== 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:"​ (e.g .mrc, .tif)
 +  - 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,​ this option has a positive effect. By defaut this option is activated.
 +
 +==== 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,​overlapping filament) 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.
 +
 +**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 =====
 +
 +
 +
 +
 +
  
  • striper.txt
  • Last modified: 2020/03/02 11:45
  • by twagner