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Histochemistry NeuroanatomyMiscellaneous utilities

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John Kiernan's Files

Files containing directly available information (text, tables, pictures) will be displayed if you click on the highlighted link , just as you do for every other web site.

Files with names of the form filename.zip are archives made with the PKZIP program. When you click on a link to an archive (.ZIP) you will be invited to download the file. Each archive contains several compressed files. To use a .ZIP archive you must download it and then decompress it (with PKUNZIP, WINZIP or a similar un-archiving program). PDF (portable document format) files require the Adobe Acrobat Reader. If you don't have this free program, click here to download it.



The files fall into three groups:

Histochemistry

1. Utilities for chemical calculations:
  • Molecular weight of an entered formula
  • Molecular weight and isoelectric pH of an entered peptide sequence
  • Interconversion of concentrations (molar, gm/100ml etc) based on molecular formula

2. Practical instructions with explanations

  • Fixatives
  • Protective film for slides
  • Stains
  • Mounting media
  • Frequently asked questions


3. Links to other web sites

  • Biological stains
  • Histochemistry
  • Histology
  • Immunohistochemistry
  • Microtechnique

Click here   for more information about the histochemistry and histotechnology files and links for downloading.

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Neuroanatomy

The University of Western Ontario employs me to teach this subject.
  • Pictures: Structure of the nervous system in a wide range of animals
  • Notes and lecture handouts
  • Slide shows for selected topics
  • Annotated drawings: Neuroanatomy and diseases of the brain and spinal cord
  • Interactive tutorial program: Development and adult anatomy of the human nervous system and special sense organs
  • Multiple choice questions: Human neuroanatomy
  • Short-answer questions: General, human and comparative neuroanatomy
  • Glossary: Look up neuro-words, including eponyms
  • Anatomy & Cell Biology 535b: Graduate half-course in human and animal neuroanatomy at the University of Western Ontario. Timetable for 2001-2002

Click here   for more information about the neuroanatomy files and links for downloading.

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Other Goodies

These are utilities for people who know how to use DOS. Most were written and compiled with ASIC (Version 5). ASIC is a dialect of BASIC written by David Visti. It generates very small .COM or .EXE files that run quickly and efficiently.

The files include:

  • General purpose utilities. Screen clearing and saving. Exchange names of 2 files. Obtain square roots. Print address centred on envelope.
  • Programming utilities. Display all ASCII line and block characters on one screen. Show decimal and hex values of colours. Find free space on disk. Draw using ASCII characters. Invert an ASCII image up-down or left-right.
Each utility is accompanied by an explanatory plain text (.DOC) file. Most also have built in help. For these  files to work under the most recent Windows operating systems (64-bit Vista or Windows 7), it is necessary to install DOSBox, a free (public domain) emulation program. Click here to get the latest version of DOSBox.

Download files:

General utilities (JKGENUT.ZIP, 15824 bytes)

Programming utilities (JKPRGUT.ZIP, 50993 bytes)


Click here  for more information about ASIC, including programming and library files for downloading.


Histochemistry and histotechnology files

Utilities for chemical calculations.  These include three programs that calculate data about entered chemical formulae. For example, if you enter:   MW NaHCO3  the formula and molecular weight of sodium bicarbonate will appear on the screen as  NaHCO3  84.00687.  This result can be sent to a comma-delimited database file if desired.
   With the solutions utility you could type
  SOLUTION  H2NCONH2  6.5M  and obtain the concentration of 6.5M urea in various units, including 39.04 grams per 100 ml. You can also use SOLUTION to obtain molarity from grams per litre or percent w/v.
   For a peptide sequence,
  PEP  gly-lys-trp-arg   tells you that this tetrapeptide has molecular weight 545.67 and that its pI is approximately 8.7.
You will need to install the DOSBox emulation utility (free download) to run these utilities on a computer with Windows 7.
Download chemical utilities. DOS version (66513 bytes)

Download chemical utilities. Windows version (164427 bytes)

FAQ: Staining, histochemistry and histotechnology.  An indexed collection of frequently asked questions on 84 topics, grouped in 6 major categories. Some topics include more than one question and answer. Many are documented with references to books and other publications. Several people have contributed answers, many of which have appeared on the Histonet listserver. This FAQ is a single quite large file (220 KB) so it may take a minute or two to load by way of a telephone connection. Once loaded, movement among its links is instantaneous. This FAQ will be updated from time to time. Consult the FAQ
HistoTech.  This DOS program generates instructions for making solutions or carrying out staining methods. When the program is started by entering the command  HT  the user is presented with a choice of menus (alphabetical or by type) and invited to select an item such as Bouin's fluid or Luxol fast blue for myelin.  The program makes a plain text file containing instructions for making the fixative or doing the technique (including making up all the solutions used). A text file can be edited or printed using any word processing program or text editor.
   The database is not complete, but worksheets can be prepared for scores of solutions and techniques, including a few that aren't in all the textbooks. Unfortunately this program refuses to run on computers with 700 MHz or faster processors (and DOSBox does not solve the problem).
Download HISTOTEC.ZIP (93625 bytes)
Keeping sections on slides.  A review of the approaches to this old problem: positively charged slides (APES, polylysine); adhesives (especially chrome gelatin); and other tricks too. Read about adhesives for keeping sections on slides.
Coating slides with nitrocellulose (= celloidin or collodion).  Detailed instructions for encasing slides in nitrocellulose film to prevent removal of sections by harsh liquids such as alkalis and hot acids. Includes references. Read how to treat slides with nitrocellulose.
Making your own aqueous mounting media.  Instructions for making aqueous mountants. Why buy, when it's cheap and easy to make your own? Originally published in Microscopy Today, and reproduced with permission. Recipes and instructions for 4 aqueous mountants.
Formaldehyde, paraformaldehyde and glutaraldehyde.  What they are and what they do. A short review of how aldehyde fixatives work, with chemical schematics and references.  Originally published in Microscopy Today, and reproduced with permission. Read about formaldehyde and glutaraldehyde.
How to stain motor end plates.  A brief overview, with references, of combined techniques for acetylcholinesterase activity and the terminal branches of motor axons in skeletal muscle.  Originally published in Microscopy Today, and reproduced with permission. Read about staining neuromuscular innervation.
Formaldehyde fixation and immunohistochemistry. An article that appeared in an NSH regional newsletter in 2005, explaining the actions of formaldehyde and why this fixative often impairs subsequent application of immunohistochemical methods. (PDF file) Read about actions of formaldehyde on antigens
Antigen retrieval. Another article that appeared in an NSH regional newsletter in 2005, discussing procedures for unmasking antigens in sections of formaldehyde-fixed tissue. The possible mechanisms of several antigen retrieval procedures are discussed. (PDF file) Read about antigen retrieval
Click here for some links to histological, histochemical and histotechnical web sites.


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Neuroanatomy files

Anatomical foundations of neuroscience.  This is an HTML text file with links to more than 60 images. It is based on handout notes (about 115 pages when printed) for a graduate half-course (Anatomy 535b) given at the University of Western Ontario. The notes explain the cells of the nervous system, developmental and comparative neuroanatomy and regional and functional anatomy of the nervous systems of man, the rat and some other animals. This file, with its links to pictures and tables of data, is designed to be read on screen.

Anatomical foundations of neuroscience

Neuro-Slides.  These are sets of images used in lectures to medical, allied health sciences and graduate students. Each set is a stand-alone .EXE file that displays the images on screen or with an LCD projector. (Needs Windows 9x, NT, 2000 or XP.) Click here  for a list of slide-shows with descriptions and instructions for downloading.
Dissection of the human brain.  Instructions for dissecting the human brain may be read on-screen, or you may prefer to download the zipped text file. There are references to photographic illustrations in Barr's The Human Nervous System: An Anatomical Viewpoint, 8th edn by J. A. Kiernan (Philadelphia: Lippincott, Williams & Wilkins, 2005 ISBN 0-397-58431-8 ). These photos show many stages of the dissection and also stained sections of the cerebrum, brain stem and spinal cord. Dissection of the human brain (On screen)

Download compressed text file BRNDISS.ZIP (27261 bytes)

Neuro Quiz.  A collection of about 300 questions, grouped by subject. Answer by typing a word or short phrase. The correct answer is then shown and explained.
This program works well in a DOSBox window in Windows 7.
All the files from the NEUROQUIZ.ZIP archive must reside in the same directory. The command  BQ  starts the program. For more information read the text file BQ.DOC

Download NEUROQIZ.ZIP (341055 bytes)

Neuro-MCQ.  About 140 multiple choice questions in Neuroanatomy. They can be chosen in groups by subject or at random from the whole collection.
This program works well in a DOSBox window in Windows 7.
A single file, NMCQ.EXE, is all that is needed to run this program.

Download NEUROMCQ.ZIP (31043 bytes)

Anatomy & Cell Biology 9535b.  A graduate half-course in human and animal neuroanatomy at the University of Western Ontario. Timetable (January-April 2008)

Read the timetable on screen


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Last updated: February 2010