(The index displays strangely. There is nothing I can do to fix the macro that generates the content)
Space Index
Total number of pages: 198
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0-93D Scanning at NPLPerforming a 3D Scan with NextEngine and ScanStudio by: Chase Shelburne NPL Home Projects Home MeshLab NextEngine Website http://www.nextengine.com
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AAccession NumberAccession records in Specify help us track important legal and provenance information- the Accession Number is the index number for that record. These numbers are formatted to show the year the material was accessioned, and the order in which it came.The
Alphabetical Index
(The index displays strangely. There is nothing I can do to fix the macro that generates the content)
Angie's Protocol - Creating new hotkeys
It is helpful to open the option for setting keyboard shortcuts under the edit menu. In the menu bar of Photoshop, under the 'Edit' header, you'll find an option for Keyboard shortcuts. Clicking this option opens an interface that allows you to fully cust
Angie's Protocol - Photoshop Scrips instructions
Post processing stacked shot images uses a variety of scripts. There used to be 5 scripts, but now we're down to 4. These scripts are found on the JSG-NPL drive at this location: DocLib\code_and_scripts\PhotoshopScripting\NSF_Scripts\Production There are
Angie's Protocol - Using Photoshop with NPL scripts
This is not an all inclusive Photoshop tutorial. In this wiki, we are going to concentrate on how NPL uses Photoshop to process images. For this tutorial, we're going to assume the photograph you are working with has a color card, showing the black and wh
Appendix A - Measured Sections: Names, Localities, Previous Workers
Carboniferous Biostratigraphy, Western San Saba County, Texas Robbie Rice Gries, B.S. Thesis The University of Texas at Austin, May 1970. [In the PRC-122 library] These sections were correlated by Rice and corespond to sections studied in the papers list
Appendix B - Key Localities
Carboniferous Biostratigraphy, Western San Saba County, Texas Robbie Rice Gries, B.S. Thesis The University of Texas at Austin, May 1970 [In the PRC-122 library] These locations were correlated by Rice and corespond to location tags from a number of pape
Attaching Images to Specify
Please use the online version of Specify to attach images. If you use the desktop version of the software we will first need to make some changes in your desktop preferences settings. Go to http://specify.npl.tacc.utexas.edu/specify http://specify.npl.ta
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CCarboniferous location codes from San SabaCarboniferous Biostratigraphy, Western San Saba County, Texas Robbie Rice Gries, B.S. Thesis The University of Texas at Austin, May 1971. In the pocket of the thesis, which can be found in the PRC-122 library, is an excellent map that in conjunction wi
Catalog Number
Consists of three sections. The first indicates the Collection, the second indicates the actual catalog number, and the third is used under certain circumstances when numbers have been split between two or more Collection Objects. Specify requires that al
Catalog Numbers at NPL
Basic Format Catalog numbers at NPL are unique. Specify will not let you save 2 Collection Object records with the same catalog number. The format is pretty simple, and the catalog number field on the data entry form won't let you save an incorrectly form
Cataloger
This is the name of the person who is creating the record in Specify. The date is the date the record is created. catalogerDateCataloged.jpg
Chronostratigraphy Tree
Entries in this tree control the available options in the Chronostrat and Biostrat fields in the Paleo Context section of the main data entry form. The Chronostratigraphy tree shows the names of geologic time in a nested format. Erathem/Era, System/Per
CO subform: Collection Object Attributes
This sub-form is important for sorting and organizing large datasets. Because NPL uses a single database for all its collection, this is where we organize our collection data into mineral, invertebrate, micro-fossil collections etc.., We also record other
CO subform: Collection Object Citations
Whenever a specimen has a type status, whether it be a holotype or simply a referred or measured specimen, you need to record the title of the article that published the information about the specimen. This lookup field searches on the first few words of
CO subform: Conservation and Specimen Prep
CO subform: Determinations The determination subform is where we define the taxonomic details of the specimen. This is much more than simply stating the genus and species- type status, taxon qualifiers, synonyms and the like are recorded here, also. One key concept here is you can
CO subform: Inventory and Preparations
All this data we can have in Specify is not really very helpful if we can't find the specimen we're looking for. Inventory and Preparations is where we record where in the collections you can find a specimen. InventoryAndPrep.jpg NPL Home https://wikis.
Collecting by Decade
In case you want to know when collection was active for the various collections and by the various collectors. Can help with pinning down maps from the appropriate time period. Collections Collection 1810 1820 1840 1860 1870 1880 1890 1900 1910 1920 1930
Collecting Information
This page deals with both the embedded subform (part of the main CO form) and the full table. Entering data into the CI subform ties it automatically to the CO you are working with. Entering data into the independent table does not. Using the data table i
Collecting Remarks
Remarks written on the label by the original collector concerning the collecting event, and can include pretty much anything that the collector wrote down for whatever reason (examples: elevation, depth, climate, other species that were found along with t
Collection Labels
Originally compiled by Jennifer Olori, June 2006-August 2008. From Word document: Z:\DocLib\Database Notes\DatabaseNotes_IMPORTANT IBR This seems to be the Wallace brachiopod collection in cabinets 263 and 284 in the PRC-122 main room. NOTE: they do not
Collectors
Search by last name. Do no make assumptions as to who this is. Only add a collector if the person is clearly listed as a collector on the label. Do not assume that the owner of the collection was the collector. For example, the label may say that the spec
Compliance Guidelines
NPL strives to provide a safe working environment for all it's staff and volunteers. Personal health and safety must come before anything else, no matter what the job. It's not just wearing the right shoes and knowing where PPE is found- it's also creatin
Conservation Information
Conservation Information covers actions taken to ensure the protection and proper care of a Collection Object. Actions such as whitening a specimen for photography, and the subsequent removal of the white smoke are Conservation Information. Also, chemical
Convert UTM
Converting from Universal Transverse Mercator (UTM) to decimal degrees. Michael Smith, 11 Aug 20922 Louis Zachos provided us with a table of locality data (as a csv file) for his sites in UTM format, some NAD27 and some NAD83. I found a Python package tha
Cooper-1970
Stratigraphy and Paleontology of Escondido Formation, Maverick County, Texas and Northern Mexico. John Doyle Cooper https://wikis.utexas.edu/pages/createpage.action?spaceKey=specify6&title=Cooper-1970&linkCreation=true&fromPageId=228820857. UT Geology Di
Creating a Change Request
To submit a change request: NPL Home Next: The Change Log ChangeRequest.jpg 1) Select the Change Request form 2) Enter the date 3) Last name of the person making the request 4) Please include your email 5) Select which category the request belongs in
Creating a Loan- Digital Image Loan
When possible, NPL prefers to send high quality digital images of fragile specimens, specimens from the Type Collection or collection objects that are being visually evaluated (as in the case where 25 corals are being checked for mineralization, and only
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DData standards at NPLThis document is intended to provide a structure for normalizing data. It is by no means an exhaustive treatise on the topic, nor is it an authority. It is simply this- if you want to get your data into a standard order, here's what NPL did, how we did it
Detailed reference
For advanced users Data Tabs: Collection Object
Digital Dataset Publishing
This document shows how NPL created standardized data sets for publication with GBIF, VertNet and other data aggregators. It is up to the individual content providers to ensure the quality of the data that they provide. I am basing the categories off of t
Direct data entry- from a drawer
Specify is a complex database, but we've put together a couple of workflows to help our experienced volunteers enter data directly into Specify. This is a simplified data entry process, but it still gets all the important information into the database in
Dissertations in Geology Library
Listed below are documents we may need to look up in order to get more accurate georeferencing data. NOTE: Blue highlighted ones in the PRC-133 library or that have already been downloaded into Z:\DocLib\GeoReferencing\Resources\Theses. Some pubs are in
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EEquipment MaintenanceKeeping the prep lab equipment running properly is everyone's priority. Expensive equipment cannot always be replaced immediately, so in order to keep our equipment lasting as long as possible, please follow the instructions for cleaning and routine care
Equipment Manuals
Air abrasion unit: AccuFlo Micro-abrasive Blaster Product Brochure http://www.comcoinc.com/wp-content/uploads/2012/06/accuflo.pdf Nozzles and abrasive media http://www.comcoinc.com/wp-content/uploads/2012/11/NozzlePowder.pdf Maintenance FAQ's http://www.c
Extending a loan
When a loan comes due, alert the Collection Manager or Curator. They will decide if a Recall or Extension letter is to be sent. If an extension is to be offered to the borrower, you must first edit the loan record. We edit the record first for two reasons
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FField Notebook-Main section detailsName: Name of the book. Please follow the format Notebook owner last name + Start Year + Geographic feature (one word) Start and End date: date of first and last entry in the field notebook Owner: Author and/or owner of the book Location: brief descriptio
Field Numbers at NPL
FIeldNumberGraph.jpg
Form alterations reference
Main Form Changes: (remember to re-import them to the correct level. ) Adding the 'Purpose of Loan' dropdown to the Loan form. in paleo.views.xml <columnDef>105px,2px,105px,1px,90px,2px,90px,4px,90px,2px,135px,4px,115px,2px,95px,0px,10px,p,p:g</columnDef>
Fossil Inventory
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GGeo-referencing ResourcesTools that we have found especially useful are marked with a ♦. Note training resources at the end of this page. Essential Tool for Locations and Radius of Uncertainty Geolocate http://geo-locate.org/web/WebGeoref.aspx - ♦ Tool linked to Specify location
Geo-referencing Solutions
County Numbering - CRITICAL Texas County Numbering is a word doc that lists the lab standard for mapping from numbers to counties. Good to print out and keep handy. Or, you can view them in the wiki at Texas County Numbering. Specimen Prefixes and Number
Geography Tree
This tree is not to be altered. The Geography tree can be a little confusing when it comes to locations outside the US. In order to fit everything into the structure, some strange side effects happen such as England being listed as a State. Geography.jpg
Getting Started with Google Refine (now OpenRefine)
Start by downloading the .zip file located at: Refine http://code.google.com/p/google-refine/downloads/detail?name=google-refine-2.5-r2407.zip&can=1&q= This download link is currently active, although the project is migrating to github. Check with the pr
Google Refine recipes for spreadsheet prep
A great link for learning Refine, written by Javier Otegui http://about.me/jotegui - https://docs.google.com/document/d/1w7yTY7gRmqGbph4_kZV4fR64Bmn5odfbiFgOmqsRwQY/edit#heading=h.bsrik76besgy https://docs.google.com/document/d/1w7yTY7gRmqGbph4_kZV4fR64Bm
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HHand written notesRegardless of the type of information you are recording, whenever you print something on a label, a sheet of paper, or a note to be placed in a drawer, ALWAYS PRINT LEGIBLY. Print in all uppercase letters; use script only if your handwriting is very very
How to Write a Locality
In Specify, the Locality Name should be a unique reference to a specific locality (also called a "named place"). It can be different from the Verbatim locality, and it often will be very different. This document is for writing a Locality Name based on any
How-to articles
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IImages: Non-Type SpecimensImages: Organized by Taxon Images: Preparations Images: the Others-Recent Marine, Gems and Minerals, Meteors and Tektites Images: Type Specimens In the collections The Non-vertebrate Paleontology Laboratory (NPL) is known for its rare and important specimens with a type and figured collection of over 22,000 specimens, and for its innovative approaches to the management of an unconventional collection. The NPL was f
In the computer lab
All staff and volunteers at NPL must have an active EID. For instructions on getting an EID, see the UT EID Self-Service Tools https://idmanager.its.utexas.edu/eid_self_help/ Much of the work at NPL involves computers. Even tasks that start in the collect
In the prep lab
The prep lab is sectioned off from other parts of the lab. There are many reasons for this- noise from the air scribe, dirt and dust kicked up from cleaning fossils, and water spray from the rock saws are the top reasons, but there are many more. Please b
Intake of borrowed material
When staff, faculty or adjust researchers want to borrow material from another institution, they do so through the Curator/Director of Operations. Material from other institutions is held in the type room in a research drawer for the requesting person. Up
Introduction
Introduction Detailed instructions for procedure are based on lots of experience with different types of collections, and lots of thought as to what is needed specifically for this collection. These procedures should be followed as closely as possib
Inventory Remarks
Any remarks concerning a particular preparation. Eventually any images associated with a preparation will be linked directly to the record within Specify, but for now, if the preparation has any photographs or scans, please enter the names and locations o
IT Policy Guide
For details on the UT Campus IT Policies, check out the CIO/ IT Policies page+ http://www.utexas.edu/cio/policies/ NPL IT Policy Guide Last update: December 5, 2014 Acceptable use The policies outlined here cover the use of NPL-owned information techn
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KKeeping it cleanThe general collections area The floor and all horizontal surfaces in the collections area should be kept free of dust and dirt. This is an ongoing problem in building 33 due to the open nature of the collections cages and the daily truck and automobile t
King Brachiopod Locations
Extract of names and King localities from: Permian Brachiopods of West Texas G.A. Cooper & R. E. Grant Smithsonian Institution Press, 1972 Available as pdf from https://repository.si.edu/handle/10088/1945 https://repository.si.edu/handle/10088/1945 OCRed
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LLabelsThe repository holds a vast collection of fossil and geological specimens. Many of these specimens have their original labels in the tray with them, and its not unheard of for one specimen to have 3 labels and a handful of scraps of paper with various not
Liath's Protocol - Creating New Hotkeys
In the menu bar of Photoshop, under the 'Edit' header, you'll find an option for Keyboard shortcuts. Clicking this option opens an interface that allows you to fully customize hotkeys for all the toolbar options, as well as Application menus for everythin
Liath's Protocol - Photo Processing with Photoshop
Before using this protocol you will need to create a few hotkeys. If you have not already done this, go to Liath's Protocol - Creating New Hotkeys Also, you will need to have your units set to mm. To check go to Edit --> Preferences --> Units & Rulers,
Lithostratigraphy Tree
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MMetadata Standards at NPLAs part of the Specify Image Attachment Protocol, you were introduced to Metadata- namely copyright and keywords. There is much more data that can be added, and the more metadata that gets added, the more useful the images are. Keywords help us search wit
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NNPL Collections-Organization of the collectionsCollections of fossil specimens can be organized in any of several different ways. Small, personal size collections (usually less than several thousand specimens) are often organized taxonomically. This makes it easy for the researcher to locate groups cu
NPL Collections-Returning Specimens to the Collections
Placing the specimen in a tray The specimen should be placed in the smallest tray possible, with the following proviso: The specimen should not touch any of the sides of the specimen tray. If a specimen tray is too small, the sides of the tray may abrad
NPL Common tasks
At NPL there are a handful of tasks that come up with some frequency. Everyone's first day involved some foam cutting- and that's one of the common tasks that you may be asked to do again. You can find links to the specific projects under the topic header
NPL Conservation Introduction
Fossils and geological samples are not as stable as people think. Chemical reactions with the environment, swelling and contracting with humidity and temperature, and poor aging properties of consolidants are among the top offenders for damage of specimen
NPL Document Library
The NPL Document Library is a large directory found on the npl-jsg file share. Everything from digital reference libraries, research papers, MSDS sheets and other administrative paperwork is found here. For the most part, documents created as part of acti
NPL Document Library- Administrative Documents
The AdminDocs directory is where most of the master copies of paperwork at held, as well as other files useful in the day to day operations of the lab. If, for example, you are filling out accession paperwork and you accidentally hit save instead of save
NPL Document Library- Person-specific
We each have our own user folders with default App data (usually hidden) download, documents folders, among others. They are held in the C drive, in the Users folder. You cannot access another users folder. Navigation Next NPL Document Library- Person-s
NPL Document Library- Project Documentation
In the formal business language of project management, there is a concept known as 'bus-proofing'. Among technical communities, it's called 'raptor proofing' based on the 1993 Classic Jurassic park. Think of it like this. If the only person who knows ho
NPL Document Library- Reference and Help Documents
Reference documents come in a couple of varieties. NPL has a large PDF library scholarly articles ranging from fossil prep and conservation articles, to scans or digital downloads of publications that mention our specimens to copies of talks and research
NPL Image Library
NPL has a multitude of special projects that involve generating images. The type specimen photography project, microfossil scanning, and photographic drawer inventory generate terabytes of data. Add to this the administrative photos (like the photographic
NPL Image Library- Project Specific
Many of the image based projects will have their own sub-folder in the Projects folder. Once these projects are completed, these sub-folders are moved to the general file structure as a new file, or merged with an existing one. Some projects, like the Lif
NPL Image Library- Specimen Images
THIS DATA NEEDS TO BE UPDATED. PLEASE DISREGARD AND SEE LIATH FOR INFORMATION The Specimen images category casts a wide net. Specimen image folders are frequently named for their type designation, taxon, the place where they were found, or the project tha
NPL Image Library-Administrative Photographs
Images that fall under this category include photos associated with particular internal procedures like accession and intake, checking in of borrowed material, cataloging damage to buildings and more. Also, you will find photographic inventories of exhibi
NPL Label Visual Guide
LabelGuideFlat.jpg
NPL Labels- Access database Generated Labels
Access generated labels: These Primary Specimen Label is the specimen label generated using data from Access databases, or other 'pre-Specify' databases. This label will be displayed with the fossil in the specimen tray. All information on this label will
NPL Labels- reference labels
Printed NPL numbers: NPL numbers reference the general NPL catalog. This is not a physical catalog, but a database detailing what information is associated with which catalog number. These labels are often printed on slips of heavy paper, and placed in th
NPL Labels-Current Primary Specimen Label
Migration from our many Access databases to a single database allowed us to solve some of the issues with non-standard data standards that were present. Labels have been redesigned to improve 'at a glance' data, improving efficiency of finding specimens a
NPL Loans-Creating a Class/Lab Loan
NPL provides specimens for a handful of labs on campus. These loans are slightly different from regular loans in that they are for a semester instead of 6 months. (Check the academic calendar http://registrar.utexas.edu/calendars to find out semester star
NPL Macrophotography Equipment
Illustrated Inventory and HowTo-1.jpgIllustrated Inventory and HowTo-2.jpgIllustrated Inventory and HowTo-3.jpgIllustrated Inventory and HowTo-4.jpgIllustrated Inventory and HowTo-5.jpg Photography Home NPL Home
NPL Non archival materials found in the collections
The process of removing all non archival materials from the collection is a long, and very expensive ongoing project. Old cabinets are replaced with metal ones whenever possible, cardboard boxes and other paper products are swapped out for archival equiva
NPL Photography- Ammonium Chloride whitening
NPL_62056___a2.jpg Whitening Agents: Ammonium Chloride (http://www.sciencelab.com/msds.php?msdsId=9927431 http://www.sciencelab.com/msds.php?msdsId=9927431) Magnesium Oxide (http://www.sciencelab.com/msds.php?msdsId=9927216 http://www.sciencelab.com/ms
NPL Prep Lab: Tool inventory
Prep Tools: Hand tools can be found against the N wall in the chest of drawers. Larger tools are hanging on the peg board. Most compressed air tools at NPL are stored in the on top of the equipment cabinet in the red toolbox. These tools, replacement pa
NPL Preparation Introduction
Preparation – procedures used in the field or in an institution to enhance the utility of a specimen or object for a particular use (SPNHC, 1994). In paleontology this frequently involves the removal of the rocky matrix in which fossils are embedded and s
NPL Preparation- Training
Anyone using equipment must be up to date on EHS Lab Safety training module OH 201 http://www.utexas.edu/safety/ehs/train/courses.html#oh201, as well as have a completed OH 102 checklist on file. Currently, NPL does not have a formalized preparation train
NPL projects
From tech-heavy gadget driven projects to getting-your-hands-dirty inventory with a pencil and paper, NPL has project for everyone. Here you'll find the current goings-on of NPL. As projects change or get completed, the list will be updated. In the comm
NPL Projects- Type Room Inventory
Inventory at NPL is normally done either directly into Specify, or by filling out printed inventory sheets. This page will focus on the database direct method. To set up the query, you'll need to download the saved query to your desktop. TypeRoomInventory
NPL Protocol and Procedures
CasualLogo.jpg NPL wiki- how to use this wiki Day 1 Orientation Click Here Health and Safety General NPL Guidelines Select one of the buttons below to explore by broad category, or find a specific project or task. Still can't find what you need? Try
NPL Specify Database: Editing an existing record
Tasks like Geo-referencing, updating specimen records and adding additional inventory information all require the user to edit an existing record. For large projects, the project manager will provide a data set, or a query to create a data set, that will
NPL Specify Reports- Outgoing Loan Invoices
OutgoingLoanReports.jpg There are 2 types of Outgoing Invoices. The Digital loan invoice is the report used when high resolution images are sent instead of physical specimens. NPL Loan Invoice is used for traditional loans where physical specimens are
NPL Specify Reports-Loan invoice (returning)
Once you've checked in a returned loan, and marked them all accounted for in the database (and filled in the date closed!) you can now run the necessary reports. From the reports tab, select the NPL Loan Invoice. A query interface will pop up (it's slow,
NPL Specify: Generating Labels
NPL task- Conservation Records Keeping track of what is done to a specimen to maintain it is vital. This conservation history is just as much part of the specimen data as the locality, collector and taxon. To ensure ease of access to these records, this information can be added straigh
NPL tasks- Daily Activity Log
Each day, you are expected to fill out the activity log recording what you worked on and for how long. This information helps the Curator gather quantifiable project information, which is crucial for writing grant proposals. You can find the Activity L
NPL Tasks- Foam Cutting
All drawers and specimen trays will be lined with polyethylene Ethafoam® or equivalent foam padding. This is an archival quality plastic foam. The surface of the foam has no openings, so dust and insects cannot accumulate easily inside the sheets, as with
NPL Tasks- Packaging specimens for loan
http://0.media.collegehumor.cvcdn.com/19/76/3ac4905c4caaae23bdd79d76314db268.jpg Things happen, we all know that. Our responsibility is to package our specimens in such a way that they will have the best chance of surviving if the box is dropped, kicked
NPL Tasks- print out NPL Numbers
DO NOT print out NPL numbers until you have registered them in the Number Allocation Database. See link to the right if you are not aware of this step! In the DocLib directory, navigate to the folder Z:\DocLib\AdminDocs\Labels Open the Excel spreadsheet t
NPL tasks- Specimen label
Current specimen labels Migration from our many Access databases to a single database allowed us to solve some of the issues with non-standard data standards that were present. Labels have been redesigned to improve 'at a glance' data, improving efficienc
NPL tasks-Creating a record set
Creating a record set is a basic Specify task. First, create a list of numbers as described in the first part of the linked page. When you run the 'In' query, on the query results page, you'll see a set of icons on the upper right corner. The one that loo
NPL Tasks: Label Repair
Supplies needed: Card stock Archival quality card stock, used as a backing for damaged labels, is kept at the printing station. Other heavy weight, stiff paper can be used with the collection managers approval. Please only use cream or white backing. ATG
NPL Tasks: Specimen Numbering
Supplies needed: Pen Micron or Pigma pens should be used for writing catalog numbers on specimens. Other brands of pens and ink may be allowed, check with the collection manager before using. B-72 (Base coat) Acryloid B-72 is laid down as a base coat to
NPL Temp Label: Exhibit
Prior to 2013, Exhibit labels were filled out by hand by collections staff. This label indicated that a specimen has been borrowed for exhibit or other approved display purposes. Most exhibit specimens are at the Texas Memorial Museum or Jackson School of
NPL Temp Label: Loan labels
As of 2013, Loan Labels are handled through the reports tab on Specify. They have 2 parts- the in-house label that stays in the drawer to mark where the specimen is normally stored, and the specimen label that stays with the specimen being loaned out. We
NPL Temp Label: Missing
The repository at NPL has been active for well over 100 years, has integrated at least 8 different collections under one roof, sent out loaned specimens to every corner of the globe and has had every cataloging system from dip-pen written ledgers to state
NPL Temp Label: old style Secondary labels
OldMiniLabels.jpg
NPL Temp Label: Specimen Temporarily Moved
These labels are put in the drawer to indicate a specimen is in a different location, but not off-campus1, for a short period of time. Pulling specimens for photography, conservation or preparation are examples of when these labels are used. Also, there a
NPL wiki- how to use this wiki
During Orientation: The Orientation required reading sections are shown in GREEN text. As you start on this wiki, use the green 'next' buttons to advance the wiki. If you find yourself down the rabbit hole of additional links, use the browser back button
NPL's accession process
Accession records are comprised of not only the database record for the accession, but also paperwork that needs to be filled out by the donor, and a representative of the lab. NPL WILL NOT APPRAISE SPECIMENS FOR DONATION. DEED OF GIFT This form establish
NPL's Darwin Core mappings
In order to create the data sets required by VertNet, we have to have functional schema mappings. This is basically a translation from our field names to those of Darwin Core. Darwin core terms are in the drop down to the left, and the Specify fields are
NPL-Texas Cretaceous Collection Orginization
NestedOrginizationNPLCretaceous.jpg
NULL- Refine Help
*In my experience, Refine wants to launch only from the Desktop. Drag the whole folder there and leave it.
Number of Pieces
Enter the number of pieces you have in your preparation. This is not necessarily the same as the number of specimens. For example, a bivalve specimen most likely be composed of two pieces. If your preparation contains two bivalve specimens, then you most
Numbering Schemes for Locations and Specimens
<county number>-T-<site number> When geo-referencing you will often encounter locality numbers of the form 122-T-13. These specific NPL sites are recorded in card files in the curator's office. You may see these locations for other states and those card
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OObject ConservationRepairing damaged labels
Other Catalog Numbers
You will often see other numbers written on either the specimen or label, or both. These numbers need to be entered here, separated by a comma. otherNumbers.jpg
Oversize
As drawers and cabinets are upgraded and shuffled around, large specimens that once fit in a drawer may now find themselves in need of re shelving. When a specimen is permanently moved to the Oversize shelves, this label is filled out and kept in the orig
Overview
NPL is a great opportunity for staff and volunteers to learn new skills, gain valuable experience, and contribute to something that is part of the rich history of paleontology in Texas. A days' work can have a person ranging through diverse tasks that in
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PPage SetsPage sets will help organize field notebooks that cover large spans of geography and time. Page sets can be scanned and bundled and attached at the bottom of the page sets section. This is not always necessary, as field notebook pages is where the bulk of
Permanent Exhibit and Permanent Loan
Labels with this title indicate that the specimen has been loaned permanently to an institution. The state of Texas does not allow state property to be given away. Therefore, any specimens that fall under this classification are considered still to be pro
Photography at NPL
NPL has developed many digitization initiatives. Our Type Collection, the Mussel Collection and many others have been digitally imaged under such projects. In 2014 we hosted a Paleo Digitization workshop with iDigBio (the digitization hub for biological c
Photography at NPL- Photosimile Lightbox
Photography at NPL- Stacked Image Troubleshooting Camera and Lenses: Power to the camera Make sure power cord is in good condition. At the end that goes into the battery slot in the camera, there is a 90° bend that can fray and short out. Check the surge suppressor- if it gets switched off, none of the e
Photography at NPL- Stacked Shot Photography
NPL specializes in high quality, pixel dense photography. It is a time consuming and exacting practice, but the results are amazing. The specimen in the image below is about 1 3/4" long. 6 pictures were taken, each at different focal planes. These 6 photo
Photography at NPL- tips and tricks
Tips for good stack series: Use brush to gently dust off any dirt on specimen. Finish with the hand-pumped air blower. Stubborn lint, especially visible on whitened specimens, can be plucked off with tweezers. Set the high point a little above what you th
Photography at NPL-Helicon Focus Tips and Tricks
HeliconFocus: When combining images, HF works best when the image slices in the selection list are in the correct order and same orientation. If they are not, the blending may not work. Auto loading the set from Helicon Remote reduces this risk Flickering
Photography at NPL-Multi-focal plane photography
Photography at NPL-using Helicon Remote software Setting up Camera Body 1) Set Mode Dial to M (Manual) **Make sure the lens set to Manual Focus, and the dial on the top of the camera is set to “M” a) Quality: set to Raw (this gives full resolution images in raw Canon format) b) Set Custom
Prep Records
Keeping track of what is done to a specimen to get it ready for storage in the repository, in a display case or photographed for publication is vital. This preparation history is just as much part of the specimen data as the locality, collector and taxon.
Proactive digitization-field data
Improve the data you collect in the field, use this digital format for more effective incorporation into our database Step-by-step guide Details of each field will be visible on the template Here's what we would like to see come in from the field-at a mi
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QQuerying Multiple Catalog Numbers in SpecifyFor this process, it is assumed that catalog number are already in Specify format. If this is not the case, please see the Google Refine Recipes for spreadsheet prep page, and scroll down to the 'Catalog Number Formatting' section. using Excel or Refine,
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RRanches and Found PlacesThese two tables, locations prefixes and locations, represent some that were tricky to track down. Note that many of the maps that are included as figures in a publication often have explicitly marked locations, especially those like 120-T-24 (e.g. count
Recalling a loan
When a researcher does not return a loan of their own accord, a recall notice may be sent. The collection manager is the final word on if a loan is up for extension or recall. When the time comes to recall a loan, run a report for loan recall and attach i
Reference Library
Research on Campus Loan Not all loans are shipped. Often enough, researchers come to visit the collections. While there is a benefit to having open access to the collections, whenever possible we try to have researchers isolate specimens they'd like to look at when they come vis
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SSearching the NPL Protocol and Procedures wikiGeneral Searching In the upper right of the wiki page, there is a search bar that can be used to find pages either the NPL wiki, or across all wikis. This searches titles of pages, so as long as you keep the terms general you can find most pages. WikiSear
Simple Database table relationship
Lets look at a few fields in the main Collection Object (CO) Form. When a data table is embedded in the main collection object form, it is called a subform. Different subforms link to the main Collection Object form in a variety of ways. They also can lin
So I have a task assigned to me...now what?
Generating a report, either for your own reference or to email to the task assignee, makes keeping people looped in much easier. The benefit of using a report, instead of interacting with the Change Request form, is the report is read-only. This way, you
Specify Data tab- Agent
For all it's 007 sounding vocabulary, 'agent' is Specify's way of saying person or organization. This table is where we keep names, addresses and other pertinent information. The agent file links to many other tables giving us a table populated with names
Specify Data tab- frequently used forms
CO_Icon.jpg CE_Logo.jpg Here is where you can learn about the frequently used forms associated with the data tab. Collection Object https://wikis.utexas.edu/display/specify6/Specify+Data+tab%3A+Collection+Object: all of the information about a specimen
Specify Data tab: Collection Object
Here's what the Collection Object form looks like as of April 2016. Keep in mind, Specify is a 'living' database, and there are always upgrades and tweaks being made. All efforts will be made to keep this page up to date. One of the first things to real
Specify Data tab: Field Notebook
Scans of field notebooks are saved in Specify as attachments, and the general data is filled out in the Field Notebook form. FieldNotebook.jpg Field Notebook-Main section details Page Sets Individual Pages
Specify Data tab: Journal
Specify Data tab: Reference Works NPL's type collection is always growing. As a result, there will always be a need to add new citations to the database, which then get tied to individual collection records. The Reference Work table is where all the citation information is stored. R
Specify Data tab: Specimen Prep
In this context, specimen preparation means actions taken to either get a specimen ready for being housed in the repository or for specific research. Some examples would be opening a field jacket and using an air scribe and other tools to free the specime
Specify Database
Please use the Specify Quick Guide http://www.liath.com/specify/quickGuide.html for basic data entry. . New to databases? Check out this primer on how it all fits together! About Specify 6 http://specifysoftw
Specify Database: Geo-reference localities
If you'd like training for Georeferencing, please see Liath in the back office for training. Georeferencing Tasks - How-to. Approaches to solving specific georeferencing problems. Georeferencing Resources - Links to numerous online resources to help with
Specify Field: about the Containers field
L is field-testing this feature, so please ask questions and note your observations. Our feedback will help the Specify team understand how paleo collections use this field. Containers, in this context, signify a relationship between separate Collection O
Specify Image Attachment Protocol
For most uses, follow this protocol. If you need to do a full metadata update, please use VRA metadata tool. Four steps: (Click on the header to expand the section) NPL Home https://wikis.utexas.edu/display/specify6/NPL+Protocol+and+Procedures Metadata Ho
Specify Import Attachment Tool
Specify has a tool that you can use to mass import images. Please don't use this unless you've added metadata to the images first. By clicking on the Attachments icon in the top tool bar, you can access the tab that lets you do mass uploads as well as oth
Specify Interactions Tab
The Interactions Tab encompasses the legal and logistical end of Collections Management. Of the tasks listed in the side bar, only a handful are common enough to warrant teaching everyone in the lab how to do them. These tasks are: Creating a Loan Checkin
Specify Interactions Tab- Accessions
Accessioning is a term used for the act of making an official acquisition of an object. Accessioning at NPL involves both analog and digital records. Physical records such as the Deed of Gift and Acquisition Checklist are filled out by the donor, scanned
Specify Interactions Tab- Creating a Loan
Tracking loans is important not only so that we know where our specimens are, but also so that we can have a record of how much use our collection gets. These numbers are vital to supporting grant requests, as well as internal tracking. The steps to creat
Specify Interactions Tab- Permit
Field trips taken under the auspice of collecting fossil specimens for NPL must have proper documentation. Casual collecting* (as defined in in the 2009 omnibus land management act, linked to in the right hand margin) does not require permits. Collecting
Specify Interactions- Borrowed material
Open Specify and click the Interactions tab. From the left hand options column, select 'Borrow'. Borrow_Form.jpg 1) The Invoice number comes from the lending institutions paperwork. It can be an invoice number or loan number. 2) This is the due date tak
Specify Interactions- Return Loan
When checking in a returned loan, care must be taken to verify each specimen sent is returned, and no specimens have been damaged. Carefully unpack the loan, setting the specimens on to a work surface near a computer. Lay the specimens out in numeric orde
Specify Labels- On Loan
All specimens that leave the lab have to have loan labels. We don't send out original labels with specimens- too much can go wrong. What we do instead is use a double-label technique that is automatically generated in Specify. These labels are tied to a q
Specify Queries- adding Tables to the sidebar.
MoreTablesToQuery.jpg The side bar you see when you open a query tab is the default view. If you click on the 'More Tables' option, you can see the additional tables you are allowed to query But what if you need to query a table that is not
Specify Query tab- advanced
Specify if capable of handling complex queries. The more complex the query is, the more comprehensive your understanding of data structure must be. First, lets take a look at the make-up of the query. AnatomyOfAQuery.jpg 1) This is the table you are askin
Specify Query tab- Basics
Many of the day to day queries have already been written and can easily be imported into your Specify workspace. To import them, follow the directions below. For creating your own queries, see the Advanced Queries page. Advanced Queries https://wikis.utex
Specify Quick Guidebook
This document is meant to be a quick reference for volunteers doing inventory and basic data entry. For a complete guide to Specify, please refer to NPL Specify guide. The Collection Object Form This form is the main data form of the Specify database. Her
Specify Reports Tab
ReportsTab.jpg Reports Extending a loan https://wikis.utexas.edu/display/specify6/Extending+a+loan Intake of borrowed material https://wikis.utexas.edu/display/specify6/Intake+of+borrowed+material NPL Specify Reports-Loan invoice (returning) htt
Specify software Set-up and Preferences
Specify, once installed on your computer needs a couple of 'tweaks' before it's really ready for full use. First, look at the top of the window- you'll see 4 menu headers: File, Edit, Data, System Tabs and Help. Click the Edit option, and select 'Prefere
Specify Tabs: Trees
The data structure for a handful of tables in Specify is organized into a nested structure, somewhat similar to the nested file tree of your computer. In the Specify world, it provides a series of sub-diving information organized as nodes within columns.
Specify Tasks- Printing and Saving Reports
Saving Loan-based Reports The Specify 'Save' interface requires you manually navigate to the folder you want. The default is the users desktop. To save directly to the loan folder, click the save icon. In the Save dialog window, select the drop down arrow
Specify tasks-Specimen Relocated
This label is created to record the specimen numbers of specimens that have been removed from a particular drawer. This label will remain in the drawer from which the specimen was removed. 'Moved' labels tell collections people where the specimens are now
Specify Tasks: Printing Labels
Collection Object Label Printing This process starts at the NPL tasks: Specimen Label page. Printing out Specimen, Exhibit, and Missing labels all follow these steps. Exhibit labels are to be printed on high quality glossy paper, or heavy card stock. Ask
Specify Workbench
This page assumes you have a .xls ready to upload. Ideally, datasets should be uploaded to the test database prior to introduction to the production database. This helps ensure no surprises are introduced into the production environment- only 'clean' and
Specify-Specimen Remarks
This section of the Collection Object is reserved for things listed on the label that does not fit into any of the other remarks sections. Information like
Specimen handling
The specimens themselves are irreplaceable, so you must be constantly careful not to drop, bang, crush, or otherwise damage them. Most damage to fossils occurs by inattention, or haste, or ennui. If you feel you are at the point of falling asleep, or are
Specimen Relocated Labels
You can't generate Specimen Relocated Labels until you've edited the specimen records themselves- including adding your self as the inventory person, and adding previous location to the Inventory and Preps sub form. Once this is done, you'll need a list o
Storage Tree
Navigating the Storage Tree StorageTree.jpgEach column shows a nested level associated with how we store our material. Each building is broken up by room, then by aisle and so on. The numbers in parenthesis indicate the number of specimens tied directly
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TTaxon TreeThis tree is not to be altered by anyone expect the Curator or senior staff members. If you are trying to enter data, and the genus or species are not in the tree, put the taxa in the Data Entry Issues field.
Texas County Numbering
1. Anderson 2. Andrews 3. Angelina 4. Aransas 5. Archer 6. Armstrong 7. Atascosa 8. Austin 9. Bailey 10. Bandera 11. Bastrop 12. Baylor 13. Bee 14. Bell 15. Bexar 16. Blanco 17. Borden 18. Bosque 19. Bowie 20. Brazoria 21. Brazos 22. Brewster 23. Briscoe
Texas County Numbering
1. Anderson 2. Andrews 3. Angelina 4. Aransas 5. Archer 6. Armstrong 7. Atascosa 8. Austin 9. Bailey 10. Bandera 11. Bastrop 12. Baylor 13. Bee 14. Bell 15. Bexar 16. Blanco 17. Borden 18. Bosque 19. Bowie 20. Brazoria 21. Brazos 22. Brewster 23. Briscoe
Texture overlay in MeshLab
Creating a Texture Overlay in MeshLab by: Chase Shelburne NPL Home Projects Home 3D Scanning Stacked Imaging Specimen Whitening Step 1: Open the model and save as a .ply file I:
The Change Log
The change log is an embedded sub-form in the Change Request form. This form is for recording technical details about implementation. Because it is embedded in the Change Request form, it's handy to know how to search for a specific record. The Search Rec
Tool Maintenance-Air Abrasion
Before use: Check the hoses, connectors, and media reservoir. If you need to add blasting media, or change to another type, clear the hopper before starting the machine. Pull and release the cleaning mallets two or three times. Check the desiccant before
Tool Maintenance-Air Scribes
Air Scribes: Before every use: Air scribes should be lubricated once per day with a drop or two of air tool oil- either in the back of the tool or in the end of the air hose. When the air pressure valve is opened, let it run for a few moments, pointed awa
Training
Type Room Inventory Query (BACK) <queries> <query name="TypeRoomInventory" contextName="CollectionObject" contextTableId="1" isFavorite="true" named="true" ordinal="32767" appversion="6.6.00" smushed=""> <fields><field position="1" fieldName="Cabinet/Shelf unit" isNot="false" is
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UUpload metadata toolWhen faced with a folder full of images that have very little in common, the best way to insert metadata is to use the modified Visual Resources Association (VRA) upload tool. The updated version of this tool install the Import/Export option directly into
Uploading data via Workbench
Select the Workbench from the top of the Specify page. On the left hand side of the page, you will see a list of available Actions, Reports and Data Sets. Select 'Import Data'. You will need to navigate to where you saved the 95-2003 Excel workbook. Once
UT Envrionmental Health and Safety
The university EHS offices can be contacted at 512-471-3511 Monday through Friday 8AM-5PM. EHS will periodically inspect the lab to make sure everything is up to code. They also manage all of the safety training classes. You are welcome to take training m
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VVerbatim LocalityThis is EXACTLY how the locality info is written on the label. Always enter ALL of the verbatim info here. All data not listed in TagSurv's locality name should be placed in brackets. Ex: Shoal Creek, Austin, Travis ???[Travis County, TX, USA 33.000, -100
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WWest Texas Brachiopod Location NamesThese locations are from "Permian Brachiopods of West Texas", G.A. Cooper & R. E. Grant, Smithsonian Institution Press, 1972, pp. 127-8. The document can be downloaded from their repository https://repository.si.edu/handle/10088/1945. Quoting from that d
Windows- Pin programs to taskbar
At the bottom of the monitor is the task bar. Programs and applications pinned to the task bar can be launched with a single click. They are much like a shortcut in that they remove the need to navigate to a frequently used program or file. Any program ca
Windows- show tags for files
Showing tags for each folder can be helpful for knowing where to save a file, as well as searching for a particular file. Follow the steps detailed below to turn Tags on for all the folders in the file tree. Navigate to the DocLib or ImageLib. ShowTags.
Windows-Create Shortcut
The easiest way to navigate NPL's file system is to create shortcuts and drag them to your desktop. Just navigate to the folder you will be using often, right-click on it the select Create shortcut. This will create a shortcut at the bottom of the file li
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YYou made it!NPL relies on volunteers and student interns to fill a variety of niches. There is so much to do, and so much to learn. You may not always be able to bring a task to completion before being assigned a new task. This is quite normal! NPL has priorities it
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