New additions to MacStereology 2.8
================================
In addition to the usual small modifications and corrections I have introduced a few new options:Ð

Align
=====
A complete stack can be aligned automatically (x- and y-shift) from the ID of a reference object.  in the Align dialogue, select the object ID then click ÔAlign by IDÕ.  You will be prompted before the data is changed.  (I do not know what happens if the data is also rotated.)
Alignments can be ignored, whilst still being kept in the data file.

Offset
======
Individual objects in a frame can be moved around from the ÔEdit dataÕ dialogue.  They can now also be dragged from the main display of any frame.  Press the Control key down and drag an object by its centre of gravity.  The measured offset will be displayed in the top right corner of the screen.
MacStereology now offsets the profiles correctly whilst being drawn from tablet.

Linkage dialogue
===============
Two additional buttons ÔSplitÕ and ÔJoinÕ have been added to enable individual profiles to be subdivided/rejoined.  Thus, where an object on the next frame links to a small feature on the current frame it is possible to define the part of the profile that it should join to.  This was done by hand in the ÔBlood vesselÕ data file, but this is a cumbersome way of reconstructing the surface.  

To split a profile, first display the frame and select the feature in the central image panel then click  ÔSplitÕ.  The full profile will be redrawn, marking every point around its perimeter.  

The mouse is then used to cut off a section with a straight line.  Press the mouse button at the start of the cut off Ð the nearest point on the profile will be used.
 
Keep the mouse button pressed down and move the mouse into the profile so that MacStereology can identify which part of the profile is being split off.  After 1 sec (4 x Wait time Ð tablet menu) this will be marked with a cross & a beep.  

Next, with the mouse button still pressed, move back to the end point on the profile and release the mouse button.  A straight line across your profile will be drawn and the new profile of that part displayed.  This new object appears in the data file and can be listed or the data editted.

If any of the mouse points are outside the image frame, or the timed point is not within the profile the operation is abandoned and the data left unchanged.  Note that this new profile will now appear in the data file as an extra object in that frame (hence there must be spare room in the data file), but it uses the same coordinates as the original profile.  It will be given a new ID number.  At present there is no check that it matches the ID on subsequent frames, so it may be necessary to change its ID from the Edit data dialogue.  Edit data can also be used to make the new feature a open line, rather than a closed object.  The difference is that the closed object includes points for the straight line.

When a new profile of this kind is no longer required it can be removed using ÔJoinÕ.  Select the extra profile then click ÔJoinÕ button.

Extra features are added directly into the data array and will retained even if the ÔCancelÕ button from Linkage is pressed.  This feature has not been extensively tested, so may still contain some bugs!  Use with care after data collection is complete on a copy of your data.

Zooming in and out and centring
=============================
In the main display and any dialogue where the profiles of a frame are displayed it is possible to zoom in or out (by a factor of 2) by pressing the ÔShiftÕ or ÔOptionÕ key then clicking the display.  In dialogues it is possible to centre the display with a ÔCommandÕ click.  In the main display, if part of the display is selected by defining a window with the mouse it is possible to make this fill the screen from the Options menu (Redraw will change to Zoom).  Similarly with ÔShiftÕ or ÔOptionÕ keys pressed Redraw will change to ÔGrowÕ or ÔShrinkÔ.  The amount of zoom is limited by the need for integer arithmetic and, on a large screen, may just possibly result in an overflow that will upset the display.
Zooming also works with the 3-D display, although, as the movement is only approximate it may be necessary to drag the display to the exact position.

Thickness & Magnification
========================
All the values in a data file can be changed simultaneously from the Thickness or Magnification dialogues.

Goodies
=======
Each layer in a 3-D reconstruction can be annotated by its frame number as well as the object IDs.  This should make it easier to identify a particular feature within a 3-D reconstruction.

Support for MacStereology
========================
I welcome you comments and suggestions about improvements to MacStereology.  If possible I will try to incorporate any ideas.

For technical support, or information about sales, upgrades or new versions (PC and PowerMac versions are under develpment) please contact me (Chris Powell) as follows 

email	cmpowell@rmplc.co.uk

phone	(44) 01865 777486

mail		Formal Software Engineering
					20 St Omer Rd,
					Cowley,
					Oxford  OX4 3HB,
					England.

There is an up to date demo version of MacStereology of the NIH-archives (zippy.nimh.nih.gov) in the directory /pub/nih-image/programs.