[Nhcoll-l] has anyone automated the counting and/or measuring of specimens from photos?

[Adam Cohen (Univ. TX)]

Counting fish and measuring (smallest and largest) specimens in each jar
has become part of our standard procedure. Unfortunately it is one of the
most time consuming steps in our workflow. I am looking for ways of
speeding this up. Has anyone tried using counting apps like CountThings (
https://countthings.com/en/). I tried it and was not initially impressed -
counts were way off. But, they are now developing a fish specimen counting
template based on ~50 specimen images I sent them. So now I am starting to
seriously consider how we might include this in our workflow. Are there
other apps out there being used to count specimens? Are they accurate?

Perhaps there are programs out there that allow automated measuring of
specimens based on images of specimens that also include a scale bar? I
started exploring ImageJ (https://imagej.nih.gov/ij/index.html), which does
this via a multi-step (multi click) process and unless it can be applied in
bulk somehow, I think it will take more time than using calipers by hand. I
see there are a bunch of plugins that I have not begun to explore.

To date our counting and measuring has always preceded cataloging so that
we can get those data included in the database and printed on our formal
jar labels. I am now imagining, cataloging and leaving those fields
empty initially while we photograph the contents of each jar, developing an
archive of images. Then, periodically we could apply a procedure to the
images in bulk that would extract counts and ideally measures.

I'd be interested in any thoughts about any aspect of this topic.

Adam

-------------------------

Adam E. Cohen
Ichthyology Collection Manager
Biodiversity Collections <https://biodiversity.utexas.edu/collections> (Texas
Natural History Collections), University of Texas,

10100 Burnet Rd., PRC176/R4000
Austin, Texas 78758-4445 U.S.A.

Phone: Cell: 512 970 2479 | Office: 512 471-8845 | Lab: 512 471-4823

Websites: TNHCIchthyology
<https://biodiversity.utexas.edu/collections/ichthyology> | Fishes of Texas
<http://www.fishesoftexas.org/home>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.yale.edu/pipermail/nhcoll-l/attachments/20211117/b8a5bbf3/attachment.html>