riedl@cs.purdue.EDU (John T Riedl) (04/12/88)
My wife is working in a neuro-biology lab that frequently needs to
measure volumes of parts of brains and spinal cords. Their current
approach is to slice the brain into cross-sections, draw on paper an
outline of the interesting part of each cross-section using a drawing
microscope, compute the area enclosed by each curve using a mechanical
digitizer, and approximate the volume by summing the areas of the
cross-sections. The lab is considering alternate approaches that
would speed up this process.
One possibility would be to buy a digitizer pad for their PC. With
software support, the digitizer could combine the steps of computing
the areas and approximating the volume. The software could also
provide a three dimensional rendering of the complete figure, which
would help in avoiding errors. Other possibilities include getting a
camera digitizer that could digitize the image directly from a
microscope, thus avoiding the drawing step.
Do any of you have experience with these or other methods for
approximating volumes during histology? I would appreciate leads on
hardware, software, and alternate methods.
Thank you,
John Riedl
{ucbvax,decvax,hplabs}!purdue!riedl -or- riedl@mordred.cs.purdue.edu
--
John Riedl
{ucbvax,decvax,hplabs}!purdue!riedl -or- riedl@mordred.cs.purdue.eduaa2@h.cc.purdue.edu (Bryan Putnam) (04/13/88)
In article <3830@medusa.cs.purdue.edu> riedl@cs.purdue.EDU (John T Riedl) writes: >My wife is working in a neuro-biology lab that frequently needs to >measure volumes of parts of brains and spinal cords. Their current >approach is to slice the brain into cross-sections, draw on paper an >outline of the interesting part of each cross-section using a drawing >microscope, compute the area enclosed by each curve using a mechanical >digitizer, and approximate the volume by summing the areas of the >cross-sections. The lab is considering alternate approaches that >would speed up this process. I'm sure that this has already been considered, but why not just drop the brain into a fluid and measure the level change? -Bryan Putnam OFFICE: Room B090 MATH User Services Programmer ARPANET: aa2@j.cc.Purdue.EDU Purdue University Computing Center BITNET: BFPUTNAM at PURCCVM Mathematical Sciences Building USENET: j.cc.Purdue.EDU!aa2 West Lafayette, Indiana 47907
chiaravi@silver.bacs.indiana.edu (Lucius Chiaraviglio) (04/13/88)
(This messed up the first time I tried to post it, I think -- sorry if anyone gets it twice.) In article <3830@medusa.cs.purdue.edu> riedl@cs.purdue.EDU (John T Riedl) writes: >My wife is working in a neuro-biology lab that frequently needs to >measure volumes of parts of brains and spinal cords. Their current >approach is to slice the brain into cross-sections, draw on paper an >outline of the interesting part of each cross-section using a drawing >microscope, compute the area enclosed by each curve using a mechanical >digitizer, and approximate the volume by summing the areas of the >cross-sections. The lab is considering alternate approaches that >would speed up this process. > >One possibility would be to buy a digitizer pad for their PC. . . I have a simpler and cheaper solution to offer. Simply submerge the sample whose volume you want to measure in isotonic buffer (to avoid having it expand or contract due to osmotic effects, and to avoid damaging it). The container you do this with should be graduated, or, if the graduations on containers useable for this are not accurate enough, it should be filled to just the point of overflowing, with things arranged so that all the overflow goes into a graduated cylinder. The rise of fluid level in the first case, or the amount of overflow into the graduated cylinder in the second case, is the volume of your tissue sample. If samples are very small but damage to the samples is not a problem, you could use an organic solvent like hexane, which wouldn't give as much surface tension problems as aqueous solutions (less viscous) -- note however that highly fluid organic solvents also evaporate rapidly in an atmosphere that is not saturated with solvent vapor (not an insurmountable problem if the stuff is decently far down in a narrow graduated cylinder, and if drafts are kept away -- the solvent vapors are heavier than air, and will build up to near-saturation in the graduated cylinder in a short time. >Do any of you have experience with these or other methods for >approximating volumes during histology? I would appreciate leads on >hardware, software, and alternate methods. I do not have any experience with this method, but it is simple enough and cheap enough that they are definitely worth a try. Besides, it is tried and true -- some Greek discovered it thousands of years ago. (-: :-), but it's true. >Thank you, > >John Riedl >{ucbvax,decvax,hplabs}!purdue!riedl -or- riedl@mordred.cs.purdue.edu -- Lucius Chiaraviglio chiaravi@silver.bacs.indiana.edu lucius@tardis.harvard.edu (in case the first one doesn't work) -- -- Lucius Chiaraviglio chiaravi@silver.bacs.indiana.edu lucius@tardis.harvard.edu (in case the first one doesn't work)