[Geoinfo] Fwd: [geo-metamorphism] Virtual Petrographic Microscope and ImageMatrix remote teaching software

Mie Mar 18 13:53:40 -03 2020

---------- Forwarded message ---------
De: Marcos García Arias <marcosgarias en gmail.com>
Date: mié., 18 mar. 2020 a las 9:49
Subject: Re: [geo-metamorphism] Virtual Petrographic Microscope and
ImageMatrix remote teaching software
To: <GEO-METAMORPHISM en jiscmail.ac.uk>

Hi all,

There is also another virtual microscope, the United Kingdom Virtual
Microscope (https://www.virtualmicroscope.org/content/uk-virtual-microscope)
that displays thin sections of rocks of the UK. It has zoom, PPL and CPL, a
tool to measure distances, and two to three places for each thin section
where you can rotate the stage and the the extinction of some specific
minerals. The good part is that this is not a software but a web-based
tool, so no need to download anything (and thus no compatibility problems);
the bad part is that it doesn´t have a tool for image analysis.

Hope this tool help us during these difficult times.

P.S. Disclaimer: I am not the owner nor the creator of this tool. I've just
found it a few weeks ago for an ongoing project.

El mié., 18 mar. 2020 a las 7:13, TETLEY MICHAEL (<
michael.tetley en univ-lyon1.fr>) escribió:

> Hi Craig,
>
>
>
> Unfortunately, it appears that 32-bit applications are not supported
> anymore in MacOS Catalina (and VPM is a 32-bit application) – so I think
> this may be the source of the difficulty you are having. There are
> workarounds available such as using a virtual machine such as the free
> Virtualbox for Mac (https://www.virtualbox.org/) or the not-so-free
> Parallels (https://www.parallels.com/uk/products/desktop/) to install an
> older version of MacOS that does support 32-bit applications (like Mojave
> 10.14 for example which I am using here), then installing and using VPM in
> this environment.
>
>
>
> I found these instructions as to how to do this (despite the somewhat
> patronising use of the word “novice” by the article author):
> https://www.winytips.com/open-run-32-bit-apps-macos-catalina-fix-needs-be-updated-error/,
> but please bear in mind I have not tested what is suggested here, so I
> can’t guarantee the outcome!
>
>
>
> This is a different problem to the security limitations enforced as
> described in this article:
> https://osxdaily.com/2016/09/27/allow-apps-from-anywhere-macos-gatekeeper/
> (which is far easier to get around!)
>
>
>
> Hope this helps and good luck,
>
> Mike
>
>
>
> *From: *Craig Storey <craig.storey en port.ac.uk>
> *Date: *Wednesday, 18 March 2020 at 12:44
> *To: *Metamorphic Studies Group <GEO-METAMORPHISM en jiscmail.ac.uk>, TETLEY
> MICHAEL <michael.tetley en univ-lyon1.fr>
> *Subject: *Re: [geo-metamorphism] Virtual Petrographic Microscope and
> ImageMatrix remote teaching software
>
>
>
> Hi all
>
>
>
> Has anyone with a Mac tried to install VPM and been told that the
> developer needs to update it to work with this version of MacOS? I am
> running 10.15.3 (Catalina). I really hope I can get this to work as I am
> going to take home a microscope with digital camera and a load of thin
> sections to recreate some of my 2nd year metamorphic practical work.
> However, the only decent home computer I will have is this Mac! Any insight
> greatly appreciated.
>
>
>
> Cheers
>
> Craig
>
>
>
> On Wed, 18 Mar 2020 at 10:11, TETLEY MICHAEL <michael.tetley en univ-lyon1.fr>
> wrote:
>
> Dear colleagues,
>
>
>
> In support of the uniquely difficult geoscience teaching circumstances we
> all currently face - for those of you who teach any kind of petrographic
> microscope-based analysis labs / classes we thought it may be helpful to
> share two options we use to do this for remote students and for setting
> remote (at-home) assessments: (1) the *Virtual Petrographic Microscope*
> (VPM) and (2) *ImageMatrix*:
>
>
>
>    1. VPM is completely free and runs locally on the user’s computer (Win
>    + Mac), allowing them to perform standard microscope thin-section analysis
>    (like zooming, stage rotation, XPL/PPL etc) – but also allows for scaled
>    grid overlays, annotations and has an export function so students can email
>    and attach their annotated analysis of a given sample for assessment. The
>    VPM software plus a large dataset of rock thin-section samples can be
>    downloaded from:
>    https://www.mq.edu.au/about/about-the-university/faculties-and-departments/faculty-of-science-and-engineering/departments-and-centres/department-of-earth-and-planetary-sciences/virtual-petrographic-microscope
>
>
>
>    1. ImageMatrix is a new online 2D image analysis platform building on
>    VPM that is currently in development. Although still in beta (a new GUI is
>    on the way shortly!), a functional pre-release testing version has been
>    made available here: https://imagematrix.science.mq.edu.au/ (please
>    bear in mind this tool is currently in development, so we welcome your
>    feedback!).
>
>
>
> Admittedly, this was not the ‘use case’ scenario we imagined for these
> tools, but it appears it might be very useful to some of you at the moment
> to continue petrographic practical courses during this period.
>
>
>
> Full details of each package can be found below for those interested.
>
>
>
> All the best,
>
> Mike Tetley and Nathan Daczko
>
>
>
> ---------------------------
>
> Dr Michael G. Tetley
>
> *Laboratoire de Géologie de Lyon : Terre, Planètes et Environnement
> (LGL-TPE)*
>
> *Université Claude Bernard Lyon 1*
>
> *Email: *michael.tetley en univ-lyon1.fr
>
>
>
>
>
>
>
> *(1) Virtual Petrographic Microscope (VPM)*
>
> The free software (for both Windows and Mac) plus thin-section datasets
> can be found on the Macquarie University website here:
> https://www.mq.edu.au/about/about-the-university/faculties-and-departments/faculty-of-science-and-engineering/departments-and-centres/department-of-earth-and-planetary-sciences/virtual-petrographic-microscope (For
> MacOSX users, please note that since changes in version 10.12 (Sierra), you
> may need to use the following workaround to install VPM:
> http://osxdaily.com/2016/09/27/allow-apps-from-anywhere-macos-gatekeeper/
> <https://protect-au.mimecast.com/s/yviBC91W8rCAYJzNCE289p?domain=osxdaily.com/>).
> Users need to download and install the software and also download each
> sample data set (about 100 MB each sample) in order to view and interrogate
> them.
>
>
>
> To learn more, the associated paper “*Virtual Petrographic Microscope: a
> multi-platform education and research software tool to analyse rock
> thin-sections*” can be found here:
> https://doi.org/10.1080/08120099.2014.886624
> <https://protect-au.mimecast.com/s/Bb-aC0YKgRsQrnkgU2JoSI?domain=doi.org>   -OR-
> if you don’t have access to this journal, we are temporarily sharing the
> paper here:
> https://www.researchgate.net/publication/263582067_Virtual_Petrographic_Microscope_a_multi-platform_education_and_research_software_tool_to_analyse_rock_thin-sections
>
>
>
> To make your own digital thin section for use in VPM, here is a summary of
> the process:
>
> *“To create high-resolution input image files, existing petrographic
> thin-sections from catalogues must be available, or new thin-sections must
> be correctly produced. There are many methods available to produce
> thin-sections of rocks, as this is a standard procedure in any
> petrophysical analysis. High-resolution images of the thin-sections must be
> taken using a digital camera. We used a Nikon Eclipse 50iPOL petrographic
> microscope with a Nikon DS-Fi1 digital camera to produce ~5 MB 1600x1600
> pixel JPEG2000 images in the Nikon NIS Elements-D software. Each sample set
> must consist of 20 images per rock thin-section: 10 images in
> plane-polarised light and 10 in crossed-polarised light generating one
> image at every 10 degrees of clockwise stage rotation between 0 and 90. To
> load a sample and start a VPM session, a complete set of 20 images per
> thin-section specimen is required. A text file named ‘config.txt’ must be
> included in each sample set directory. This file contains the scaling value
> for the sample set, which is generally the length of one side of the image
> in millimetres. This value is referenced by the software and used to
> calculate the scaled grid and zoom values while the program is running. In
> summary, 21 files in a folder makes one digital thin section ready to load
> in VPM.”*
>
>
>
>
>
> *(2) ImageMatrix*
>
> ImageMatrix can be found on the Macquarie University website here:
> https://imagematrix.science.mq.edu.au/ It provides realistic virtual
> teaching and learning experiences that use clustered 2D image data
> sets to simulate experiences like microscopy or comparing spatial data that
> changes with time. The web-based learning & teaching platform, ImageMatrix,
> helps educators provide authentic learning experiences outside of the
> laboratory that are flexible, inclusive, stimulating and rigorous.
> ImageMatrix also facilitates combined modality overlays from different
> instruments (e.g. BSE, EBSD, EDS, CL images can all be overlaid onto a thin
> section and turned visible and invisible in layers) and custom tools
> for image management, display and manipulation (e.g. annotation,
> measurement, etc.). ImageMatrix is therefore relevant to all image-based
> teaching (not just thin sections), along with research and outreach.
>
>
>
> The image database is closed in the sense that only a few of us have
> access to upload images to our server, but if you have a spectacular image
> dataset that you would like to share, please email nathan.daczko en mq.edu.au to
> discuss. Keep in mind that ImageMatrix is intended for all high-resolution
> 2D images (satellite, gigapan, maps, photographs, photomicrographs,
> microchemical maps, etc) and could be used to interrogate geology at any
> scale.
>
>
>
>
>
> VPM was funded by Macquarie University and ImageMatrix was funded by
> Macquarie University with support from the University of New England,
> University of South Australia, and University of Sydney, and major industry
> sponsorship from Pells Sullivan Meynink.
>
>
>
>
>
>
>
>
> ------------------------------
>
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>
>
>
>
> --
>
> Craig Storey
> Professor of Geology
> School of the Environment, Geography and Geosciences
> Burnaby Building
> University of Portsmouth
> Burnaby Road
> Portsmouth
> PO1 3QL
> UK
> +44 (0)2392842245
> Website
> <http://www.port.ac.uk/school-of-earth-and-environmental-sciences/staff/craig-storey.html>
>
>
>
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>
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-- 
Dr. Marcos Garcia-Arias
Assistant Professor in Petrology
Universidad de Los Andes
m.garcia en uniandes.edu.co
marcosgarias en gmail.com

*Links:*
SCOPUS: https://www.scopus.com/authid/detail.uri?authorId=36124834200
ORCID: http://orcid.org/0000-0002-3585-2364
ResearcherID: http://www.researcherid.com/rid/A-7595-2011
Google Scholar: https://scholar.google.com/citations?user=IWdJLncAAAAJ&hl=es
ResearchGATE: https://www.researchgate.net/profile/Marcos_Garcia-Arias

*Quote:*
Inside every cynical person, there is a dissapointed idealist (George
Carlin)
<https://www.researchgate.net/profile/Marcos_Garcia-Arias>

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Servicio Geológico MInero Argentino (SEGEMAR)
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