ramen and pickles

science, technology, and medicine served up with some tasty noodles

Minarcik Histopathology Lectures on your iPad

Dr. John Minarcik a pathologist from the midwest has created a wonderful series of video lectures on pathology and histology.


You can view the pathology course on YouTube (it has some pretty visually assaulting color schemes on the slides), or watch some of the hundreds of awesome videos about histology.  The “Shotgun Histology” videos are great short videos going over a particular slide and trying describe everything in the field of view.  If you download the videos from the website, you have to use something like HandBrake to convert the files to .mp4’s so you can put them on your iPad.


If you are watching the videos on YouTube, there are numerous websites that let you paste in a YouTube URL and convert the content to .mp4 and other formats.


I wanted to download the histopathology videos in a batch (there are tons of them) so I could watch them on portable device (like an iPad), so I wrote a script to grab them all.  This requires using some flavor of Unix and having the HandBrake command line interface (HandBrakeCLI) installed along with wget.


Here is the script:


mkdir MinarcikHistopathology
cd MinarcikHistopathology
# Get the source html with all the video links we want:
# The index.html file has all the links, so let’s use Perl to grab those links:
perl -ne ‘/li><a href=”([^”]+)(wmv)”>/ && print “http://www.medicalschoolpathology.com/HistopathologyWMVs/$1$2n”&#8216;  index.html > minarcikDownloads
# Now use wget to get all those URLs.  This will take some time.  Go get something to eat, watch some YouTube videos, etc.
wget -i minarcikDownloads
# Remove the spaces in the file names (will work for nested directories too, so is useful in general):
find . -name ‘* *’ -depth | while read f ; do mv -i “$f” “$(dirname “$f”)/$(basename “$f”|tr ‘ ‘ _)” ; done
# Run HandBrakeCLI on everything to convert each .wmv into an mp4 which run on anything.
for i in $(ls *.wmv); do
    echo ${i}
    HandBrakeCLI -i ${i} -o ${i}.mp4


One response to “Minarcik Histopathology Lectures on your iPad

  1. Pingback: Educational videos onto your iPad | ramen and pickles

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