A quick guide to thin section / slab digitization

Michael D Higgins

You will need:

• Document (photo) scanner
• One with a light in the lid for scanning slides or negatives - cost about 100-150$. I use an Epson Perfection. Resolution of 50 micrometres is possible.
• You do not need a dedicated slide scanner (3000-10000$), but you may get slightly better resolution with one.
• Transmitted light is a diffuse source
• Reflected light is NOT orthogonal - more like 45 degrees
• You can also scan rock slabs

•     Microscope with a digital camera
• If you want to do more complex work then you will need
• Corel Photo-Paint or Adobe Photoshop image treatment programs
• CorelDraw or Adobe Illustrator graphic programs

• ImageJ program or the tweaked Imagej version fiji (fiji is just ImageJ)

• ImageJ macro  plugin CSD_output.ijm (A text file; In Windows: Click right and Save as …)
• You will need to find where ImageJ is installed on your computer and install this file in the directory
• .../ImageJ/plugins or
• If you have installed fiji - then in ...fiji.app/plugins and then use 'Menu/Plugins/Install'
• It may be already there if you have installed CSDCorrections after you have installed ImageJ
• If it is installed correctly then you will see it in 'Menu/Plugins' in the list at the bottom.

• CSDCorrections program for stereological corrections

Scan slab / thin section

• Scan slab / thin section or use a digital camera on a microscope.
  
• Images can be pasted together electronically to make a mosaic. I use PTGui or Microsoft ICE (freeware) but many other programs can do this.
• Save images as uncompressed tiff files.
  

OPTIONAL If you want to get the maximum from your image then open image in Corel Photo-Paint / Adobe Photoshop.

1. Crop image (Corel Photo-Paint: Image / Crop).
2. Adjust contrast, brightness (Corel Photo-Paint: Image / Adjust / Brightness…).
3. Save image as tiff.

OPTIONAL For further image treatment open image in CorelDraw / Adobe Illustrator 

1. Make a new layer (CorelDraw: Tools / Object manager)
2. Put layer with image at the back, and turn off drawing, printing for this layer
3. Select upper layer
4. Draw outline of each crystal. Click on each corner with Bezier tool. Make sure to close the outline by clicking on the first point.
5. Select all outlines. Make line white and fill black. 
6. Export as an uncompressed tiff file, black and white. Use the same resolution (dpi) and pixel dimensions as the original image. (CorelDraw: File /Export / Tiff file)
   

Analyse image

• Open ImageJ

• Open tiff file of outlines with File/Open…
  
• If you have not changed the image file (that is it still has full colour or grey scale range) then you must threshold it to make a binary (black/white) file.
• Image/Adjust/Threshold... or /Color Threshold
• In color threshold you must select
• Threshold color = B & W.
• Close this box
  

    

• You may want to remove single pixels: Process / Noise /Despeckle

• Choose units and scale - Analyse / Set scale.
• Scale is usually in inches
• Change 'Known distance' to a scale value and unit to mm.(Here 25.4 mm = 1 inch)
• Check 'Global'.

• Analyse / Set measurements.
  
• Select: Area; Centroid; Fit Ellipse
• If you want to get the mean grey scale then check this. But you must threshold image without closing the window (ask me!)
• Set decimal places to 3 or 4
  

• Analyse the image 
• Analyse / Analyse particles.
  
• Min size 10 pixels; Check Display results, Clear results table, Exclude edge particles.
  

• This will make a table of the results.

• We now need to make a .csd file for feeding CSDCorrections.
  
• Plugins / CSD Output. This makes the data file in a log window.
• Save the file as your_sample.csd. Close Log window.

Do stereological corrections 

• Open CSDCorrections
• Open the file you have just created
• Check that Area is OK
• Check that Intermediate and Long parameters are OK. This is important as changes in I/L will affect the size scale.
• Estimate Roundness from the image (less important).
• Estimate Fabric from the rock and image.
• Press Calculate.
• Size data and graphs are on 'Size data' page
  
• Orientation and spatial distribution data are on the ‘Orientation data’ page 
• You can copy data tables and images to other programs – Word processor, Vector drawing program, Spreadsheet.