Creating a CIP site 

 

The CIPsite folder



The folder contains 4 folders

  • beauty case
  • calib
  • clut
  • DATA

 

If you want to try out CIP, download this demo CIPsite:  → demoCIP.tar.gz

If you want to check your results, download this version:  → demoCIPdone.tar.gz

Note: both demo sets have been reduced to half size after running CIP

 

 

The beauty case (optional)



This folder contains a number of TIFF images that are useful for editing the CIP results:

  • Color look-up tables for c-axis orientation images in stereographic form (POL)
  • Color look-up tables in matrix form (CLUT)
  • Scales prepared for each of the objectives and the camera that is used to acquire the input *)
  • Sinistral and dextral shear couple


*)

Here, the objectives are ZEISS Epiplan and the camera is a ZEISS Axiocam. Obviously, other camera-microscope combinations, require the preparation of other scales.

 

A beauty case can be downloaded here:  → beautycase.tar.gz

 

 

The calibration files



The folder contains a number of Text files:

  • axio-micro-660-700.CAL: general camera calibration file for wave lengths from 660 - 700 nm

     

  • incA-incP-15-660-700.LUT: calibration file for section thickness 15 µm
  • incA-incP-15-lin-660-700.LUT: same as above with emprirical correction
  • incA-incP-20-660-700.LUT: calibration file for section thickness 20 µm
  • incA-incP-20-lin-660-700.LUT: same as above with emprirical correction

 

More on calibration files:  → here

 

 

The color look-up tables (CLUT)



The folder contains color look-up tables for CIP (RAW non-interleaved RGB images, 180 · 180):

  • CIP-P-spectrum.CLUT and CIP-P-spectrum.POL
  • CIP-P-standard.CLUT and >CIP-P-standard.POL
  • CIP-P-qtz20-pale.CLUT and CIP-P-qtz20-pale.POL
  • crosspol.CLUT.raw
  • cirpol.CLUT.raw


CIP distinguishes extensions 'CLUT' (for square CLUTs) and 'POL' (for round CLUTs) and interpretes the look-up tables accordingly.

 

More on CLUTs:  → here

 

 

The DATA folder



The folder contains one folder for each sample.

 


 

 

The sample folder



The folder contains a number of folders for input and putput images, as well as the controle files necessary to operate the CIP programs:

  • input: folder with RAW input images for CIP
  • prepare: folder for preparing input
  • takes: folder containing original images, as acquired
  • CIP1A: destination folder for CIP1A results
  • CIP1B: destination folder for CIP1B results
  • CIP2: destination folder for CIP2 results
  • CIP4: destination folder for CIP4 results
     
  • y.ctrlA, y.ctrlB, y.ctrl2, y.ctrl4: four controle files

 

The input folder



The folder contains a number of RAW images. It is convenient to use extensions that indicate the nature of the file:

  • 010... 180 = rotation images for increasing degree of rotation
  • backR backT = background images for tilted and rotation images
  • cirpol = circular polarization
  • eup, nup, sup, wup = tilt images: East Up, North Up, South Up, West Up
  • nopol = unpolarized image = basis for mask


 

More on CIP input:  → here