====== 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 =====