Resectioning Image Stacks with MAPPaint
Useful Unix Commands
  1. ls - lists the files in current directory
  2. cd smpldirectory - goes to specific directory
  3. cd .. - goes back one directory
  4. rm smplefile - deletes file
  5. rm *.filetype - removes files of all of the file type specified
  6. cp smplefile smpledirectory - copies file to a directory
  7. Up arrow - Shows what command was entered previously
Converting OpenLab File or Tiff Images to Wlz Volume
  1. Save Openlab file as multiple tiff files. Make sure they are numbered sequentially with 3 to 4 significant digits depending on number of layers. *Make sure the tif images are 8 bit greyscale ( Can check in Adobe Photoshop) ** Make sure they have .tif extension can be added in OpenLab under "Naming" in save as multiple.
  2. Set the working directory in a terminal window to the folder containing the tif images. (See "Useful Unix Commands" for common commands)
  3. Type "/opt/MouseAtlas/bin/MakeVolume" and press enter. This will create a volume from all the tiff images in the present directory and name it "vol.wlz".
  4. Open up MAPaint
  5. Open Reference command and open up the wlz volume created
  6. Open up volume by hitting x-y view command under view toolbar
  7. Zoom window and hit controls button on lower left hand corner
  8. Can type in degree shift or can drag bar - adjust until optimal pitch and yaw is obtained
  9. Record desired pitch and yaw values
  1. Set the working directory in a terminal window to the folder containing the volume "vol.wlz"
  2. Type "/opt/MouseAtlas/bin/Resection" and press enter. Enter desired pitch and yaw when prompted, pressing enter after each. This command will create a folder named "p(pitch)y(yaw)" containing resectioned tif images at the specified pitch and yaw.
Scale Resectioned Images (Optional)
  1. Open a series of tiff images resectioned at either p90 or p90y90 using the "Open Multiple" command in Openlab
  2. Compare the calibration information of the original magnification with the section thickness to determine whether to shrink the x- or y-dimension. For example, a sample sectioned at 4 um using a magnification of 17.559x (corresponding to 6.0um per pixel), then resectioned at an orthogonal plane has pixels corresponding to 6 um by 4 um in the x- and y-dimensions, respectively. It therefore needs to be shrunk in the y-dimension to achieve equal scales.
  3. Calculate the new image size in the dimension being changed from the initial image size and relative pixel sizes. For example, from the example above, if the initial y-dimension is 600 pixels, it would be scaled as follows:
  4. The image dimension can be viewed and changed from the "Document Size" option under the Image Menu option in Openlab. Scale the image to the new size.