2011 Remote Sampling Protocol IN PROGRESS by xiaopangnv


									    2011 Salmon River
Remote PIT Tagging Protocol

             Prepared by:

     Quantitative Consultants, Inc
          1010 Hays Street
            P.O. Box 8623
         Boise, Idaho 83707

             Prepared for:

      U.S. Department of Energy
    Bonneville Power Administration
     Division of Fish and Wildlife
            P.O. Box 3621
     Portland, Oregon 97208-3621

        BPA Project Number:
        BPA Contract Number:

          June 2, 2011 - draft
LIST OF TABLES .......................................................................................................................... ii

LIST OF FIGURES ........................................................................................................................ ii

LIST OF APPENDICES ................................................................................................................ iii

INTRODUCTION .......................................................................................................................... 1

BACKGROUND ............................................................................................................................ 2

SITE SELECTION AND ESTABLISHMENT .............................................................................. 2

COLLECTION AND HANDLING.............................................................................................. 10

PIT TAGGING ............................................................................................................................. 13

SCALE AND GENETICS SAMPLING ...................................................................................... 19

MULTI-AGENCY COOPERATIVE ACTIVITIES .................................................................... 20

REMOTE TAGGING DATA LOGGER PROCEDURES........................................................... 20

LITERATURE CITED ................................................................................................................. 21

APPENDICIES ............................................................................................................................. 23

                                                  LIST OF TABLES


      (HARRELSON ET AL. 1994). ............................................................................................... 4


                                                 LIST OF FIGURES
FIGURE 1. EXAMPLE OF A SITE MAP ..................................................................................... 9

FIGURE 2. COMMONLY USED SITE MAP SYMBOLS .......................................................... 9

FIGURE 3. FISH HELD IN HAND IN PREPARATION TO PIT TAG..................................... 15

FIGURE 4. INSERTING THE PIT TAG ..................................................................................... 16

FIGURE 5. PIT TAG LOCATION WITHIN THE BODY CAVITY.......................................... 18


      ON CHINOOK >50 AND <60MM. ..................................................................................... 19

                                    LIST OF APPENDICES
APPENDIX A. SITE ESTABLISHMENT DATA SHEET ........................................................ 26

APPENDIX B. 2010 REMOTE PIT TAGGING MASTER DATASHEET................................ 27


APPENDIX D. PIT TAGGING DATA LOGGER PROCEDURES .......................................... 29

Columbia River Basin anadromous salmonids have exhibited precipitous declines over the past
30 years, with several populations now protected under the Endangered Species Act (ESA)
(Schaller et al. 1999; McClure et al. 2002). A comprehensive monitoring strategy needs to be
implemented to reduce the uncertainties surrounding the declines, and the strategies required to
reverse this trend. Data collected from current and historical monitoring programs are generally
not adequate or reliable enough for the purposes of ESA assessments and recovery planning
(Tear et al. 1995; Campbell et al. 2002; Morris et al. 2002). In addition, monitoring programs for
anadromous salmonids in the Columbia River Basin have typically been initiated to evaluate the
effects of specific management actions, such as the demographic effects of hatcheries. As such,
data are most appropriately viewed at the scale of the subpopulations and populations for which
they were derived. However, the ESA requires assessments of species and their habitat at
multiple spatial scales – from specific reaches, to subpopulations, populations, and the ESA
management unit of Pacific salmon, the Evolutionary Significant Unit (ESU), which is a distinct
population or group of populations that is an important component of the evolutionary legacy of
the species.

Current monitoring programs for Pacific salmon did not develop as a cohesive design, thus
aggregating existing data from a myriad of independent projects creates challenges in addressing
these spatially complex questions. These problems arise because information is often not
collected in a randomized fashion (Larsen et al. 2004), sampling techniques and protocols are not
standardized across programs, and abundance, distribution, population dynamic, and
demographic data for species and their habitat is often not available (Tear et al. 1995; Campbell
et al. 2002; McClure et al. 2002). As recovery planning has focused more effort on tributary
habitat restoration to mitigate for the mortality resulting from the Federal Columbia River Power
System (FCRPS) the limitations of historic and ongoing sampling programs have become
increasingly apparent.

The Integrated Status and Effectiveness Monitoring Program (ISEMP – Bonneville Power
Administration (BPA) project #2003-0017) has been created as a cost effective means of
developing protocols and new technologies, novel indicators, sample designs, analytical, data
management and communication tools and skills, and restoration experiments. These tools are
designed to support the development of a region-wide Research, Monitoring and Evaluation
(RME) program to assess the status of anadromous salmonid populations, their tributary habitat,
and restoration and management actions.

The ISEMP has been initiated in three subbasins: Wenatchee/Entiat, WA, John Day, OR, and
Salmon River, ID, with the intent of designing monitoring programs that can efficiently collect
information to address multiple management objectives over a broad range of scales. This

• Evaluating the status of anadromous salmonids and their habitat;

• Identifying opportunities to restore habitat function and fish performance, and

• Evaluating the benefits of the actions to the fish populations across the Columbia River Basin.


The use of Passive Integrated Transponders, or PIT tags, is one tool that the ISEMP project is
using to answer scientific uncertainties that underlie status, trend and effectiveness monitoring in
the South Fork Salmon River and Lemhi subbasins regarding juvenile steelhead (Oncorhynchus
mykiss) and Chinook salmon (O. tshawytscha). Specifically, PIT tags can be used as a tool by
which growth, survival, and migratory patterns of juvenile steelhead and Chinook can be
examined and quantified. PIT tags have been shown to have high retention (Dare 2003) with no
impact on growth or survival (Petersen et al. 1994), and are primarily used to determine the
migration timing and estimate survival of smolts migrating through Columbia River
hydroelectric projects (Achord et al. 1996), as well as smolt to adult survival of returning adults.
PIT tags have also been used successfully to monitor the growth and movement of resident
salmonids (Wipfli et al. 2003).
The goal of the Salmon ISEMP project is to measure the freshwater productivity of salmonids
for the purposes of evaluating the effectiveness of habitat actions at improving freshwater
productivity and to determine the relationships between status and trends in habitat quality and
availability and status and trends of salmonid freshwater productivity. Effectively measuring
freshwater productivity is complicated by the fact the distribution of juvenile salmonids is
largely unknown for much of their life history. Further, until recently, the application of unique
marks has been largely limited to juveniles greater than 60mm fork length. In order to address
these complexities, juvenile sampling associated with the Salmon ISEMP is distributed using a
spatially-balanced design (generalized random tessellation survey (GRTS); (Stevens and Olson
2004). This document will focus on how sampling effort is distributed, criteria for rejecting
probabilistically selected sites, and methods for juvenile capture and tagging at remaining sites.

Most sites will be selected using a list of coordinates provided by the GRTS randomized site
selection protocol and master site list. Sites in the master list will be systematically scrutinized
in order to maintain randomization to determine sampling feasibility. Some sites may be
selected in a non-random fashion to meet requests from other agencies. These will not be
considered part of the sampling frame for population estimation, but be used for site specific
objectives associated with specific local agency objectives.

The process for selecting and setting up appropriate site length is as follows:
   1) office assessment– asses the site location to determine if the site meets protocol criteria and
      falls within known anadromous waters and is physically accessible, if know;
   2) ownership determination – determine if the site is on private land and if permission for access is
      needed; contact must be made before crews scout site by project supervisor;
   3) field reconnaissance- a crew will scout the access route to site location to determine the most
      efficient travel routes for field crew;
   4) site location: determine physical point on stream associated with the coordinates obtained
      from Master Site List;

   5) determine evaluation status, if a target site continue to 6 and 7, otherwise document why it is a
      non-target site;
   6) determine site length: using width category tables determine site length; and
   7) monument site: appropriately establish bottom of reach for future crew visit.

Assessing the Site Location
In the office, using professional knowledge, associated GIS data layers, and previous ground
surveys, work to determine if the target site is feasible to sample based upon: land owner
permission, accessibility and professional judgment (no fish, gradient is too steep, no water). If
the target still looks appropriate after this first review, continue to step two. If the target is not
appropriate, document it using the codes from Table 1. If a site is eliminated for reasons that
preclude it from being populated by Chinook or steelhead it should be called a “Non Target” site
or “NT” in the Evaluation Status column in the Master Spreadsheet. If access is limited by land
owner denial or we are unable to sample a site in which Chinook or steelhead could possibly
inhabit the site, it should be called “Target Not Sampled” or “TN” in the Evaluation Status
column in the Master Spreadsheet. Explain why the target was rejected or not sampled in the
Evaluation Reason column in the Master Spreadsheet.

If a site on private land is rejected due to landowner denial, it should be replaced with another
private site. When a site is replaced, record the design number of the replacement site in the
Master Spreadsheet in the Replacement Site Design # column. Track the date of evaluation of a
site in the site evaluation forms and the Master Spreadsheet in the Evaluation Date column.
Also, make sure that an evaluator is recorded in the Master Spreadsheet in the Evaluator column.

In the field, access the target site using the coordinate provided in the Master Spreadsheet. This
coordinate location will be the middle of the site. Walk upstream and downstream of the site to
determine if it is a safe sampling location (ie… are there strainers, or rapids?). If the site is
deemed hazardous, move the site upstream or downstream. The maximum distance that a site can
be moved is 500 meters upstream or downstream. Record the reason for moving a site in the
Master Spreadsheet. If the target site location is not suitable for sampling, document the reason
in the Master Spreadsheet using the codes provided in Table 1.

At times, access to random sites may be restricted due to various events such as forest fires
(especially later in the summer), road closures, timber harvesting operations, etc. In this case,
document the reason you could not access the site, and you can attempt to sample the site at a
later date. Again, track the date of evaluation of a site in the site evaluation forms and the Master
Spreadsheet in the Evaluation Date column. Also, make sure that an evaluator is recorded in the
Master Spreadsheet in the Evaluator column.

If the coordinate does not fall on the stream, walk directly perpendicular from the coordinate to
the channel and start there. If the coordinate point lands between two tributaries, choose the
tributary closest to the coordinate location. The coordinate location will be the middle of the
site. Scout downstream and upstream of the coordinate (scout the estimated site length) and
determine if a site can be established. If a site is accepted and sampled, it will have at least one
data collection event. Be sure to record TSF or TSH respectively when a site has been sampled
for fish or habitat in the Master Spreadsheet in the Fish_Eval Status or Hab_Eval Status
columns. Record a DCE name for that site (if there are multiple DCE‟s, simply choose one) in
the Master Spreadsheet in the Fish DCE or Habitat DCE columns. The sample date will be
reflected in the DCE name. Note: If a site is not sampled for fish or habitat it will not have a
DCE Name.

Table 1. Evaluation status and evaluation reason codes.
  Code          Name                 Meaning
  Evaluation Status
  TA            Target               Scouted but not yet sampled
  TS            Target Sampled       Site is a member of the target population and was sampled
  TSF           Target Sampled       Fish sampling complete but no habitat sampling yet
  TSH           Target Sampled       Habitat sampling complete but no fish sampling yet
  TN            Target, not          Site is a member of the target population but was not
                Sampled              sampled
  NT            Non-Target           Site is not a member of the target population
  NN            Not Needed           Site is not needed
  Evaluation Reason
  PI            Physically           Site cannot be accessed by foot
  NS            Not Safe             Site is not considered safe to sample
  LD            Landowner            Access to site was denied by landowner(s)
  GR            Gradient             Gradient is determined by ground truth to be >12%
  VB            Vertical Barrier     A vertical barrier of >6 feet below the site
  NW            No Water             No or minimal water at site.
  SK            Site Skipped         Site is not sampled with no pre-approved reason for
                                     rejecting (fire closure, road closure, Chinook fishing
                                     season, crew emergency, etc…)

Determining Site Length and Width Category
To determine site length, determine the bankfull stage. Look at several indicators including: stain
lines, changes in substrate, slope breaks, tops of point bars, permanent vegetation, and debris
lines. Additional details on bankfull identification are included in Table 2 below (Harrelson et
al. 1994).

Indicators should be more distinguishable at non-constrained sites where, for example, tops of
point bars, changes in substrate, and permanent vegetation may be the most reliable indicators.
In constrained sites, especially those with boulders and bedrock substrate, indicators may be
difficult to identify.

Table 2. Indicators used to determine bankfull stage of a site (Harrelson et al. 1994).
Indicator      Description
Top of Point   The point bar consists of channel material deposited on the inside of
bars           meander bends. They are a prominent feature of C-type channels but may
               be absent in other types. Record the top elevation of pointbars as the
               lowest possible bankfull stage since this is the location where the
               floodplain is being constructed.
Change in      Look for the low limit of perennial vegetation on the bank, or a sharp
Vegetation     break in the density or type of vegetation. On surfaces lower than the
               floodplain, vegetation is either absent or annual. During a series of dry
               years, perennial plants may invade the formerly active floodplain.
               Catastrophic flows may likewise alter vegetation patterns. On the
               floodplain (above bankfull stage) vegetation may be perennial but is
               generally limited to typical streamside types. Willows, alders, or
               dogwoods often form lines near bankfull stage. The lower limit of mosses
               or lichens on rocks or banks, or a break from mosses to other plants, may
               help identify bankfull stage.
Change in      Changes in slope occur often along the cross-section (e.g., from vertical to
Slope          sloping, from sloping to vertical, or from vertical or sloping to flat at the
               floodplain level). The change from a vertical bank to a horizontal surface
               is the best identifier of the floodplain and bankfull stage, especially in low-
               gradient meandering streams. Many banks have multiple breaks, so
               examine banks at several sections of the selected site for comparison.
               Slope breaks also mark the extent of stream terraces. Terraces are old
               floodplains that have been abandoned by a downcutting stream. They will
               generally have perennial vegetation, definite soil structure, and other
               features to distinguish them from the active floodplain. Most streams have
               three distinct terraces at about 2 to 4 feet, 7 to 10 feet, and 20 to 30 feet
               above the present stream. Avoid confusing the level of the lowers terrace
               with that of the floodplain; they may be close in elevation.
Change in      Any clear change in particle size may indicate the operation of different
Bank           processes (e.g., coarse, scoured gravel moving as bed load in the active
Materials      channel giving way to fine sand or silt deposited by overflow). Look for
               breaks from coarse, scoured, water-transported particles to a finer matrix
               that may exhibit some soil structure or movement. Changes in slope may
               also be associated with a change in particle size. Change need not
               necessarily be from coarse-to-fine material, but may be from fine-to-
Bank           Look for bank sections where the perennial vegetation forms a dense root
Undercuts      mat. Feel up beneath this root mat and estimate the upper extent of the
               undercut. This is usually slightly below bankfull stage. Bank undercuts
               are best used as indicators in steep channels lacking floodplains. Where a
               floodplain exists, the surface of the floodplain is a better indicator of
               bankfull stage than undercut banks that may also exist.
Stain Lines    Look for frequent inundation water lines on rocks. These may be marked
               by sediment or lichen. Stain lines are often left by lower, more frequent
               flows, so bankfull is at or above the highest stain line.

If a site has been previously sampled, use the original width category, which will be provided
prior to sampling using the previous site information from the database. If a new site is being
established take a total of 5 bankfull width measurements. Take the 1st bankfull width
measurement where the lat/long coordinate for the site is located. Use this distance to determine
the distance you need to go upstream and downstream and take bankfull width measurements
(one each upstream and downstream). Continue upstream the distance of the width measured at
the last location and measure the bankfull width again (repeat this procedure for the downstream
measurements). Average the 5 bankfull measurements and use that value to determine the width
category and associated site length from Table 3.. Minimum and maximum site length is 160 m
and 1 km, respectively (any average bankfull less than 7.5 m will have a site length of 160 m)
(Table 3). Sample the entire length if it is possible to sample and tag all fish within a 10 hour
day. If not, only sample a length that allows all work to be completed within a 10 hour day. Be
sure to record the actual length of stream sampled and the GPS coordinates of the uppermost
point sampled as TS. Note: The 10 hour day is intended as a guideline. Sample the maximum
amount of stream possible knowing that it is ok to sometimes work over the allotted 10 hours.

Table 3. Width categories for determining the minimum site length.
                   Width            Minimum site
 bankfull width
                   Category         length (m)
 0 to 8            8                160
 8.1 to 10         10               200
 10.1 to 12        12               240
 12.1 to 14        14               280
 14.1 to 16        16               320
 16.1 to 18        18               360
 18.1 to 20        20               400
 20.1 to 22        22               440
 22.1 to 24        24               480
 24.1 to 26        26               520
 26.1 to 28        28               560
 28.1 to 30        30               600
 30.1 to 32        32               640
 32.1 to 34        34               680
 34.1 to 36        36               720
 36.1 to 38        38               760
 38.1 to 40        40               800
 40.1 to 42        42               840
 42.1 to 44        44               880
 44.1 to 46        46               920
 46.1 to 48        48               960
 >48.1              50               1000

Site Coordinates

Use the GPS receiver to document bottom of site, top of site and mid-point of site. The latitude
and longitude of master sample site coordinates will be the mid-point of the site (site-marker).
Record the lat/long for the site marker, Bottom of Site (BR) and Top of Site (TR) locations. Use
the CONUS NAD 83 datum for establishing a new site. Take two readings at each location.
1. Turn the GPS on at least 5 minutes before recording coordinates.
2. Reading must have an accuracy of <± 50m. If that level of accuracy is met, record the
    coordinates and accuracy.
3. If this level of accuracy cannot be attained within 10 min, use the GPS‟s „average
    position/location‟ function with at least 200 „measurement counts‟ to attain coordinates. To
    access this function hold down the „enter‟ button until „mark waypoint‟ screen opens and
    then press the „menu‟ button.
4. After 200 „measurement counts‟ are obtained with the „average position/location‟ function,
    record the coordinates and accuracy and write „avg. or average‟ with the accuracy.
5. For each location (BR, TR, and site marker) take the two readings/coordinates and calculate
    the average UTM coordinates.

Monument the Site
Aluminum site markers are used to monument the site location. The markers will assist others in
finding the start of the original sample site. Site markers will not be placed in designated
wilderness areas or on private land unless permission is given by the landowner; use a distinctive
feature (large spanner, snag, rock or tree) near the Bottom of Site (BR) to mark the site.

1. Locate a distinctive feature near the BR that will be easily identified.
   a. Something relatively permanent like a piece of large wood in the stream (e.g. a large
      spanner, snag, or tree).
   b. Sometimes riparian zones are characterized by a continuous patch of similar vegetation;
      try to pick something that might stand out such as a big clump of sage or one conifer near
      the start of the site.
2. Make sure marker has “ISEMP” written on it.
3. Attach one of the markers to your chosen spot.
4. Take a GPS reading of the site marker location and record it.
5. Enter a brief description of the site marker location, i.e. upstream (US) of BR 5m on River
   Left (RL) attached to trunk of large juniper.
6. Take a compass bearing from the marker to the BR and record it.
7. Measure the distance from the marker to the BR and record it.

Photo Documentation
Photos are important for documenting site condition and detecting change through time. ISEMP
will be re-sampling sites, so the photos you take will help future crews relocate sites. Photos are
one of the easier tasks that you will perform and one of the most helpful for locating the site-
take your time and take quality photos.

When taking photographs:
1. Always take the ISEMP site name and date photo first. The remaining photos can be taken in
any order.
2. Always take the photo without using the zoom and with the resolution on “better” or
3. Try and get both banks in the photo. For smaller streams stand back from the object of
interest a distance of 5 m. For larger streams (> 8 m wide) stand back 10 m or at the best distance
to assure you can see both banks.
4. Hold the camera 1.5 m from the ground.
5. Take photos with the sun at your back and not looking directly into the sun. Also, minimize
taking photos where part of the frame is in the shadows and part is in the sun. Take photos of the
following items at each site.

      Site ID/Date: Write the stream name, Design Number, and date. Use a large marker and
       take this photo first.
      Site marker location: Take the photograph looking towards the site. If in a wilderness
       area do not place a marker but choose a good distinctive feature to use as the marker and
       take a photo of it with someone pointing at it.
      Site overview: Take from a location where the greatest extent of the site can be observed.
       This is often on a hillside or terrace. Sometimes this can be difficult so try your best.
      The bottom and top of the site: Take a photograph looking both upstream and
       downstream. Stand parallel to the channel at a distance of 5 m.
      Misc. Stream: Take a representative photo of the steam channel. Make sure to get both
       banks of the stream.
      Distinctive feature: Photograph a distinctive feature that will help relocate the site for
       future visits.

Figure 1. Commonly used Site Map Symbols

 Object                Symbol                Object                     Symbol

 Site Marker                                 Fence

 Bottom of Site                              Road

 Top of Site                                 Direction of Flow

 Conifer                                     Upslope

 Deciduous                                   Cutbank

 Herbaceous / meadow                         Snag

 Forested                                    Spanner

 Stump                                       Log jam

 Large Wood                                  Pool

 Rock                                        Side Channel               SC

 Bar                                         North Arrow               N

Electronic Storage Formats
While in the field, record all data on the site description data sheet provided in Appendix A.
This data will be transferred to the associated excel spreadsheet as soon as possible. Download
photos to the computer. Scan and download the hand-drawn site map. Take a screenshot
depicting the site topographically on Maptech mapping software. Follow the naming convention
below to save this information electronically.

        Root Directory: C:\ISEMP\<subbasin>\SiteRecon\
        Sampled Site Directory: C:\ISEMP\<subbasin>\SiteRecon\<EvalStatus>\
        Sampled Site Directory: C:\ISEMP\<subbasin>\SiteRecon\<EvalStatus>\<streamname
         design number>
                Where <subbasin> is either “SFKSalmon” or “Lemhi”
                Where <EvalStatus> is either “TargetSite” or “NontargetSite”
                Where <streamname> is e.g. “Lake Cr” or “EFSR”
                e.g. C:\ISEMP\Lemhi\SiteRecon\TargetSite\Lake Cr 542\

        Site Description File– <Designnumber_Description.xls>
                        e.g. 542_Description.xls
        Site Map File(s)– <Designnumber_Map.jpg>
                        e.g. 542_Map.jpg
        Site Topo Map(s)- <Designnumber_Topo.jpg>
                      e.g. 542_Topo.jpg
      Site Photo Point File(s) – <Designnumber_(phototype).jpg>
       Where (phototype) = OVUS – overview looking upstream at bottom of site
                      OVDS – overview looking downstream at top of site
                      OV – general overview of site
                      TRSM – top site site marker
                      BRSM – bottom site site marker
                      “other” – distinctive feature designation
                              e.g. other= rock, logjam, etc.
                      e.g. 542_OVUS.jpg or 542_rock.jpg

Experimental Study Site Establishment
There will be instances where the GRTS site selection system will not be utilized, or will be
modified to experiment with study design features. In these cases carefully record all of the
parameters listed above and describe how each site was selected. Use the same data forms,
techniques, and storage naming conventions described above.

                               COLLECTION AND HANDLING
Each sampling site will be snorkeled prior to collection to determine fish presence. If no fish are
observed, finish entry the pertinent information into the datalogger and do not continue
sampling. In streams too small to snorkel, begin sampling the site using the electrofishers as if
fish are present. If no fish are present after ½ the site has been sampled, stop sampling, record the
pertinent information in the datalogger.

Three collection methods will be used: electrofishing, snorkel herding/seining, and angling.
Each collection method will be a separate data collection event (DCE) at each site sampled.
Record all pertinent information about each site and each data collection event in the data logger
according to the instructions in Appendix D. If a datalogger is not available or instructed by the
supervisor, record information on the field data sheets (Appendix B). Fish are held in live boxes
and/or aerated 20-liter buckets in which water will be frequently refreshed. Fish are tagged and
released immediately upon recovering from anesthetic. To minimize collection stress, all fish
collection, handling, and tagging activity will occur at water temperatures of less than 18º C, and
will cease when any other occurrence suggests fish are being stressed.

Sites where multiple methods can be employed, different sequences of methods should be used.
In streams where snorkel herding and seining can be employed where the seines reach
completely across the habitat units, angling should be done first, followed by seining, and finally
by electrofishing. In streams where seining can only reach parts of habitat units because of
safety or habitat complexity (pocket water), snorkel herding and seining should occur first, and
while crews are working up the collected fish, angling can occur, and then electrofishing.

Angling will be used especially in cases when other capture techniques are not efficient at
capturing all target life stages. In relatively large bodies of water with abundant O. mkiss angling
is the most effective method for capturing that species. Angling is also used in larger streams that
have a lot of pocket water (e.g. mainstem Secesh rapids at low water), where snorkel herding is
inefficient, but the streams are too wide to employee electrofishers for larger steelhead. Anglers
will use either a five-weight fly-rod and reel, or an ultra-light spinning rod. Single barbless
hooks will be used at all times. Use the smallest hooks possible for the conditions and target
species and size class.

Begin angling at the downstream end of the collection site and work upstream. Fish each site
thoroughly from bottom to top to ensure that all habitat types are sampled. Record all fish
captured. Place all target species in 20-L buckets and portage to the live boxes. Release all non
target species immediately. When all sampling is completed, release tagged fish throughout the
area from which they were captured.

Employ electrofishing in relatively small streams where difficult terrain preclude successful
snorkel herding and to successfully capture life stages unobtainable via angling. Larger streams
will require up to two electrofishers to adequately collect fish. Our primary shockers used for
fish collection are the Samus 725MP electrofishing unit; in some instances we will also use
Smith Root brand shockers and that should be noted in dataloggers or on forms. The Samus
725MP has two voltage settings, 360v and 500v - both of which are used depending on
conductivity, temperature and fish response. Set pulse width and pulse frequency to optimize
fish response while maintaining fish health. Pulse width will range from 30 milliseconds to 3.0
microseconds and frequency ranged from 40 to 95 Hz. Duration of having the shocker engaged
depends on many factors including response of fish in the field, size of stream and water depth,
as well as conductivity of the water. The Smith Root shocker will have more settings with
different value types than the Samus shockers; don‟t worry about keeping the settings equal
between the brands if the Samus doesn‟t have enough power to adequately collect fish and we
need to use the Smith Root‟s additional power.

NOTE: when using two shockers of the same brand, keep the settings equal between the units.
If using two brands of shockers, make sure both types are noted in the datalogger or on the data
forms. The shocker settings, if different between two brands, record the Samus settings in the
data logger, but document in the electro-pass notes the settings for the Smith Root.

Begin electrofishing at the downstream end of the collection site and work upstream. Crews will
consist of shocker operator, hand-netter, up to two people operating the beach seines or block
nets. In streams where electroherding takes place, set a beach seine downstream of the
electrofisher to collect “herded” fish. Collect stunned fish from the river with dip nets, place
them in 20-L buckets and portage them to the live boxes set outside the range of the electofisher.
An additional person may be designated to carry a fish bucket and spot adults or redds. If the
spotter finds adult fish or redds, the crew must cease all shocking activity and carefully move
past an adequate distance to ensure fish and egg health and safety. Hold non-target species
initially to prevent further exposure to the electrofisher, then record and release them once
shocking has ceased. When all sampling is completed, release tagged fish throughout the area
from which they were captured.

The size of the sampling crew and sequence of sampling will be determined by stream sizes. In
small, low gradient streams where one electrofisher can be used, the sampling crew starts by
placing block nets at the upstream and downstream boundary of a habitat unit and/or site
(depending on length). Two netters should assist the individual shocking. In sites with poor
footing, an additional person can be used to hold the fish bucket. In larger sites or high stream
flows, where block nets can‟t be employed, block nets should not be used as well as an
additional shocker. In these sites a seine can be employed to capture stunned fish that make it
past the netters.

Snorkel Herding/Seining
Snorkel Herding/Seining and is most feasible in pool, run, and meadow habitats where the
substrate is fine-grained and wood is sparse, and where fish densities are high. Beach seines of
various sizes are used for fish collection and the size of seine employed is determined by habitat
type, stream size and numbers of crew members. The preferred seine netting is 1/8” knotless
mesh. There are a myriad of techniques that can be employed using seines and it is important to
use each technique consistently throughout the watershed. Snorkel herding is used in relatively
slow moving water and can be the most successful method for capturing juvenile Chinook

Snorkel herding crews should consist of two people operating the beach seine, one or two
snorkelers spotting and herding fish and a person to carry a fish bucket and spot adults or redds.
Begin at the downstream end of the collection site and work upstream, first along one bank, and
then up the other, while collecting from pools in between. Once a group of fish is spotted, the
seine operators will set the leadline of the seine downstream. Snorkelers would then “herd” the
fish into the net. Fish are then scooped up by the seine operators. Use dip nets and hand nets to
scoop captured fish from the wetted seine. Place them in 20-L buckets and portage them to the
live boxes. If the spotter finds adult fish or redds, the crew must cease all collection activity and
carefully moved past an adequate distance to ensure fish and egg health and safety. Record all
non-target fish and release them downstream immediately. When all sampling is completed,
release tagged fish throughout the area from which they were captured.

For seining with multiple seines (areas with low habitat complexity and rocks/sticks/etc. to hang
up the seine, position one seine securely across the lower end of a run or pool and place a second
seine across the stream at the top of a habitat unit and move the upper seine downstream,
crowding fish toward the lower seine. You can use a snorkeler to make sure the lead line stays
on the bottom and moves over As the lead line of the upstream seine crosses the lead line of the
downstream seine, pull the lower seine up out of the water, trapping the fish. In areas of high
stream flows, or large pools where a bottom seine is not feasible. Crews should employ the
seines from the upstream direction and “swim” the seine downstream using snorkelers to herd, or
scare fish from the downstream direction as well as using snorkelers to keep the lead line from
hanging up but on the stream bottom.

Density/Population Estimation
To estimate the number of fish, we will perform either a mark-recapture or a multi-pass depletion
estimate at all of our sites. In smaller streams that allow block-netting, a three pass depletion
estimate will be performed. For larger streams we will employ a mark-recapture where the
“mark event” is the first pass and the second pass, which will occur the next morning, is the
“recapture event”. Every recapture event will be executed at full effort using the method or
methods that were most effective in the mark event. All unmarked fish will be measured,
weighed and PIT tagged in the recapture event.

Depletion Notes:
   1) Make sure fish from each pass are kept in separate buckets/live-wells and worked up
       independently. All fish will be processed entirely according to protocol.
   2) Each pass should be done with similar effort.

Mark-Recapture Notes:
   1) A small caudal fin-clip located dorsally should be used to help identify tagged fish. All
      Target species, including those too small to PIT Tag will be fin clipped, measured and
      weighed. Be sure to indicate “New Tag” or “Non Efficiency Recapture” for every “Fin-
      Clip” in the datalogger. Fish do not need to be dorasally fin-clipped in the recapture
   2) It is important to distribute the fish from the mark event equally throughout the reach to
      ensure complete mixing of the marked and unmarked fish. Avoid releasing fish in the
      lower 10% of the reach so they less likely to move leave the reach between events.

                                        PIT TAGGING
Size Range and ProceduresAll steelhead/rainbows and Chinook salmon within the target size
ranges will be PIT tagged. Size ranges for the two sizes of PIT tags include:
       Chinook –
               9 mm Tags = 50mm to 59mm
               12 mm Tags = 60mm +
       Steelhead –
               9mm Tags = 60mm – 69mm
               12 mm Tags = 70mm +
       Cutthroat –
               12 mm Tags = 80mm +

PIT tag fish using individual modified 100cc syringes and 1 1/2”, 12ga hypodermic needles
(Prentice et al. 1990). Use two PIT tag sizes, 12mm and 9mm, depending on the size of the fish.
To minimize disease transmission, disinfect all tags and all associated equipment for a minimum
of 10 min with isopropyl alcohol. Transport fish from live boxes to your streamside tagging
station in aerated, 20-L buckets with lids. Take fish from bucket and place them in an anesthetic
solution of tricaine (MS222, final concentration of about 40 mg/L) and sodium bicarbonate to
help buffer the acidic properties of the MS222. After anesthesia, sort and remove fish of other
species and target species not suitable for tagging (i.e. injured or too small), allow them to
recover, and release them back to the stream (after all passes are complete). Record the start and
stop times and temperatures in the data logger or a data sheet if necessary.
Pre scan target species with a Digital Angel FS2001, or a Biomark 601 PIT tag reader to check
for recaptures. Measure and record each fish‟s fork length (to nearest mm) and weight (to
nearest 0.1 g) and record species, and any injuries. Then inject the fish with a PIT tag following
procedures published by PTAGIS and included below. Scan each tagged fish with the reader and
record the tag information. Collect and record genetics samples according to the instructions on
page 20. After tagging, allow all fish to recover in fresh water, transfer them back to a live cage
in the stream, and hold for a minimum of 0.5 h before releasing them as close as possible to the
location where they were collected.

PIT tag Implantation
Implantation of PIT tags into juvenile salmonids will follow protocol set forth by the PIT tag
Steering Committee (CBFWA 1999). Although this document includes Steering Committee
guidelines (below), each individual should develop their own “best” technique based on hand
size, dexterity, etc.

       1. Fish Position In Hand
         The fish is held in the hand with the belly of the fish up, the tail toward your thumb,
the head toward your little finger (
Figure 2). Position the fish in your hand so the point of injection is even with your middle finger.
With a 50-150 mm fish, the head is held between the little finger and the heel of the hand. The
tail is held between the thumb and index finger. Slight pressure is applied with the middle finger
by pressing the side of the fish‟s belly. This will tighten the belly tissue so the needle will
penetrate easily.

Figure 2. Fish held in hand in preparation to PIT tag

       2. Injector position in Hand
          Both the thumb and plunger type PIT tag injectors are held in the hand in a similar
          fashion. The injector lies in the hand so the tip of the index finger rests on the barrel
          of the needle (Figure 3). The barrel of the syringe is held by the fingers, and the little
          finger rests on the flange at the top of the syringe. The top of the syringe rests against
          the palm near the base of the little finger. The index finger rests on the barrel of the
          needle. If you have a thumb type injector, the thumb will rest on the screw attached to
          the plunger. If you have a plunger type injector, the end of the syringe plunger will
          rest against the palm of your hand. (People with small hands may have difficulty
          holding plunger type injectors). The barrel of the needle rests against the heel of the
          palm of the hand holding the fish. This provides maximum support for the needle.
          You want as many contact points between you and the injector as possible. This will
          allow precise movement of the point of the needle. Without maximum control of the
          injector, the needle can penetrate too deep and damage the internal organs of the fish.
          If you are using a plunger-type injector, use the heel of the hand, rather than your
          thumb, to push the plunger. If you use your thumb, you can lose control of the needle
          and cause internal damage to the fish. Be sure to always maintain contact between the
          barrel of the needle and the heel of the hand holding the fish.

Figure 3. Inserting the PIT tag

3. PIT tag injection
   The needle should penetrate the fish‟s belly between the posterior tip of the pectoral
   fin and the anterior point of the pelvic girdle. Avoid placing the point of the needle
   too far posterior. There is a loop of the intestine under the pelvic girdle so you should
   avoid inserting the needle in that area. The puncture should be made one to two
   millimeters off the mid-ventral line. If you necropsy a fish you will see that the
   pyloric ceca and the spleen lie below the puncture wound. The tip of the needle can
   (but should not) nick either organ without injury to the fish (Prentice et. al. 1986).

    Using the middle finger of the hand holding the fish to add pressure, place the tip of
    the needle on the belly of the fish 1-2 mm from the mid-ventral line. The bevel of the
    needle is open toward the belly of the fish so the point of the needle is away from the
    internal organs. The puncture is made with a short, quick, jabbing motion. Maximum
    control is needed because the tip of the needle should move forward only about 1-2
    mm. The angle of the needle should be about 45° with the belly of the fish and the
    motion of the needle should be directed through the fish toward your middle finger.
    Once the needle has penetrated the abdominal wall, and with about 2-3 mm of the
    needle inside the fish (for fish up to about 150 mm), the tag can be injected. Using
    this technique, if you slip and the tip of the needle travels more than 1-2 mm, the
    needle will either follow the inside wall of the abdominal cavity or will pass back out
    the abdominal wall without passing through any internal organs. If you are using
    sharp needles, the puncture wound should be a straight incision about 1-2 mm in
    length. This type of wound may be difficult to see immediately after tagging and will
    heal quickly. If the needle is dull, the puncture wound will probably be a ragged hole,
    which will heal more slowly. There will also be some discoloration around the
    ragged wound that is caused from bruising of the tissue.

4. Tag Location
   The tag should be located in the ventral area of the abdominal cavity somewhere
   between the pyloric ceca and the pelvic girdle, generally in the fatty tissue just
   posterior to the pyloric ceca (Figure 4). It is all right if the tag lies under the pelvic

Figure 4. PIT tag location within the body cavity

          Small fish (45-60mm) are very difficult to hold in your hand and the point of
          insertion may need to be moved slightly forward of the posterior tip of the pectoral
          fin. This will provide a little more room for the tag in the abdominal cavity. Research
          conducted by the Nez Perce Tribe (Rabe and Nelson unpublished) suggests that the
          point of insertion of the 8.5mm PIT tag on Chinook <55mm should occur posterior
          and slightly ventral to the distal end of the pectoral fin (Figure 5) so as to avoid tag
          loss and internal organ damage.



Figure 5. Proper and improper points of insertion of the 9mm PIT tag on Chinook >50 and

Dorsal Sinus

A protocol for dorsal sinus tagging is still being developed and will be inserted here as soon as it
is complete

                            SCALE AND GENETICS SAMPLING
Sample Sizes (scales):
Steelhead: all PIT tagged steelhead, whether a recapture or newly tagged fish, will have a scale
sample taken. Preferably they will also have a PIT tag as well. Do not take scales from young of
year any fish too small to be tagged.. NOTE: fish captured during recapture event (see mark-
recapture section) will not have scale samples collected.

Chinook: Up to 300 scales samples per sub-basin (SF Salmon or Lemhi River) should be
obtained from a sample of Chinook over the course of the sampling season. Collect scales from
all fished deemed to be a yearling (residual from previous broodyear) and the largest 10% of fish
from the current broodyear and all.

Sample Sizes (DNA):
Steelhead: 150-200 tissue samples should be taken from steelhead proportionally across all
steams sampled – Mainstream Secesh, Lake Creek, Grouse Creek, Summit Creek, Zena Creek,
Lick Creek and any others sampled; and all Lemhi watersheds sampled – Hayden Creek, Big
Timber Creek, mainstem Lemhi, mainstem Lemhi tributaries with a goal of 50-75 per
Chinook: We do not need DNA samples from Chinook.

Collect scale samples from a target area of the fish defined by drawing an imaginary diagonal
line from the posterior insertion of the dorsal fin to the anterior insertion of the anal fin, and
sampling on that line just above the lateral line. Try to get 10-15 scales per sample by scraping
them with a small knife blade. Then spread them onto a piece of rite-in-rain paper and store in a
coin envelope. Be sure that each envelope is labeled with a design number stream name, sample
number, date, species, length, weight and initials of the person who collected the sample. Record
the sample number in the data logger and on the data sheet provided.
Collect genetic samples from one of the pelvic fins using scissors cleaned in alcohol before and
between sampling. Take enough tissue for each sample to equal about 3X3mm in size. Store
each sample in a two-ml plastic vial filled with non-diluted, 200 proof, USP ethyl alcohol. Store
vials upright in the storage box to keep the sample submerged. Label each vial according to the
stream and/or watershed from which they were taken and number them sequentially. Record the
sample number in the data logger.


PIT Tagging

Record all pertinent information in the Juniper Systems Allegro MS Rugged data logger
(Juniper) data loggers as the information becomes available. Chose one crew member to carry
the Juniper, and record all parameters throughout the data collection event. If a data logger is not
available or you are informed by the supervisor to use both systems, the data should also be
recorded on paper forms provided in the appendices. Data should be entered according to the
Remote Tagging Data Logger Procedures in Appendix D.

                                    LITERATURE CITED

Achord, S., G.M. Matthews, O.W. Johnson, and D.M. March. 1996. Use of passive integrated
      transponder (PIT) tags to monitor migration timing of Snake River Chinook salmon
      smolts. North American Journal of Fisheries Management 16:302-313.

Dare, M.R. 2003. Mortality and long-term retention of passive integrated transponder tags by
       spring Chinook salmon. North American Journal of Fisheries Management 23:1015-

Campbell, S. P., A. Clark, L. H. Crampton, A. D. Guerry, L. T. Hatch, P. R. Hosseini, J. J.
Lawler, and R. J. O‟Connor. 2002. An assessment of monitoring efforts in endangered species
recovery plans. Ecological Applications 12: 674–681.

CBFWA (Columbia Basin Fish and Wildlife Authority PIT Tag Steering Committee).
    1999. PIT Tag Marking Procedures Manual. Version 2.0.

Harrelson, Cheryl C; Rawlins, C. L.; Potyondy, John P. 1994. Stream channel reference sites: an
       ..... and sediment size (Leopold et al. 1964). Natural sys- ...

Larsen, D. P., P. R. Kaufmann, T. M. Kincaid, and N. S. Urquhart. 2004. Detecting persistent
       change in the habitat of salmon-bearing streams in the Pacific Northwest. Canadian
       Journal of Fisheries and Aquatic Sciences 61: 283-291.

McClure, M. M., E. E. Holmes, B. L. Sanderson, and C. E. Jordan. 2002. A large-scale,
      multispecies status assessment: Anadromous salmonids in the Columbia River Basin.
      Ecological Applications 13: 964-989.

Morris, W. F, P. L. Bloch, B. R. Hudgens, L. C. Moyle, and J. R. Stinchcombe, 2002.
       Population viability analysis in endangered species recovery plans: past use and future
       improvements. Ecological Applications, 12: 708–712.

Prentice, E.P., D.L. Park, T. A. Flagg, and C.S. McCutcheon. 1986. A Study to Determine
       theBiological Feasibility of a New Fish Tagging System. Report to Bonneville Power
       Administration,Project 83-319, Contract DE-AI79-84BP11982. 89p.

Schaller, H. A., C. E., Petrosky, and O. P. Langness. 1999. Contrasting patterns of productivity
       and survival rates for stream-type chinook salmon (Oncorhynchus tshawytscha)
       populations of the Snake and Columbia Rivers. Canadian Journal of Fisheries and
       Aquatic Sciences 56: 1031–1045.

Stevens, D.L., and A. R. Olsen 2004. Spatially Balanced Sampling of Natural Resources. J.
       Amer. Stat. Ass. 99(465):262-278

Tear, T. H., J. M. Scott, P. H. Hayward, and B. Griffith. 1995. Recovery plans and the
       endangered species act: are criticisms supported by data? Conservation Biology 9: 182-

Wipfli, M.S., J.P. Hudson, J.P. Caouette, and D. T. Chaloner. 2003. Marine subsides in
        freshwater ecosystems: salmon carcasses increase the growth rates of stream-resident
        salmonids. Transactions of the American Fisheries Society 132:371-381.


        Appendix A. Site Establishment Data Sheet
Site Number:                      Stream/Map #:                                         Date:
Time:                             Crew:
Latitude:                         Longitude:                            Accuracy:
Reach length:                     Reach width:                          Wood factor 1-5:
Estimated drive time:             Estimated hike time:                  Brush factor 1-5:
Evaluation status: TA TSF   TN                       Evaluation reason:
                                       Bottom Reach Monument:
Latitude:                         Longitude:                            Accuracy:
Marker:                           Tree DBH:                             Bank side:
Bearing to BR:                    Distance to BR:                       Photo #:
                                        Top Reach Monument:
Latitude:                         Longitude:                            Accuracy:
Marker:                           Tree DBH:                             Bank side:
Bearing to BR:                    Distance to BR:                       Photo #:
Drive directions:

Hike directions:

General Description:

Appendix B. 2010 Remote PIT Tagging Master Datasheet

Site Number:                              Stream/Map #:                     Visit #:      Date:
Lat(BR):                                  Lat(TR):                          Reach Length:
Long(BR):                                 Long(TR):                         Width Category:
                                                   Fish Collection Method
Method 1:                                 Begin Time:                       End Time:
Direction:                                Begin Temp:                       End temp:
Gear (Circle):            Electrofisher   Seine/nets               Flyrod     Spinrod       Other:

Method 2:                                 Begin Time:                       End Time:
Direction:                                Begin Temp:                       End temp:
Gear (Circle):            Electrofisher   Seine/nets              Flyrod      Spinrod       Other:

Method 3:                                 Begin Time:                       End Time:
Direction:                                Begin Temp:                       End temp:
Gear (Circle):            Electrofisher   Seine/nets              Flyrod      Spinrod       Other:

                 Pass 1                                    Pass 2                           Pass 3
Conductivity:                             Conductivity:                     Conductivity:
Volts:                                    Volts:                            Volts:
Frequency:                                Frequency:                        Frequency:
Wave Length:                              Wave Length:                      Wave Length:
Begin Time:                               Begin Time:                       Begin Time:
End Time:                                 End Time:                         End Time:
Operator:                                 Operator:                         Operator:
Begin Time:                               End Time:
Begin Temp:                               End temp:
Release date:                        Release time:                          Release temp:
New tag vial number and size:
Non-target species, number and size:
Whitefish:                           Sculpin:                               Brook Trout:
Bull Trout:                          Cutthtroat:                            Other:
Collection:                               Holding:                          Tagging:
Shed Tags:
Additional comments:

     Appendix C. 2010 Remote PIT Tagging Fish Survey Datasheet
Site Number:                          Stream & Map Number:                                        Date:
                                                             8mm                                                  Shed      E-
                                                              Tag   Recap     Scale      DNA      Injury   Mort    Tag   fishing
     Species Code   Length   Weight           Tag Number      (x)    (x)    sample #   sample #    code     (X)    (x)   pass #
Appendix D. PIT Tagging Data Logger Procedures
1. Installing and Setting up QC PIT Tagging on a Field PC:
       a. Remove all previous versions of the software using the “Remove Programs” function in the
            “System” tab of the “Settings” menu.
       b. Windows XP users:
                  i. You must install ActiveSync on your computer – this can be downloaded from the
                     Microsoft web site (go to www.microsoft.com and search for “activesync” to find
                     the download link).
                 ii. Connect the field PC to your computer with a USB cable.
                iii. After a connection is established, click on the “File Explorer” link to open a view of
                     the files on the field PC.
       c. Windows Vista or Seven users:
                  i. These operating systems have “Windows Mobile Device Center” that will open
                     when the field PC is connected.
                 ii. Connect the field PC to your computer with a USB cable.
                iii. After a connection is established, click on the “Connect without setting up device”
                     link and then under the “File Management” section click on the “Browse the …” to
                     open a view of the files on the field PC.
       d. Browse to the top level of the main storage for the field PC and copy the following files (if
            they do not already exist):
                  i. NETCFv35.wm.arm4i.cab
                 ii. PL2303_WinCE50_ARM_v1009.CAB
                iii. PITTag2011.CAB
       e. From the field PC screen, launch the “File Explorer” (in programs) and navigate to this same
            location (root level directory).
       f. With a stylus, touch each of the files to install them. They MUST be installed in the
            following order!
                  i. NETCFv35.wm.arm4i.cab
                 ii. PL2303_WinCE50_ARM_v1009.CAB
                iii. PITTag2010.CAB
       a. Optional:
                  i. Run the GPS_Information.exe on your computer to install the GPSinfo utility on the
                     field PC.
       b. Plug in the USB cable from the GPS receiver.
       c. If not prompted for a driver name, do a soft reset of the field PC:
                  i. Hold the power button down for 5 seconds
                 ii. Click the “Reset” button on the display
                iii. Wait for the field PC to complete the reset operation
       d. When prompted for the driver name, enter: USBSER.DLL

       e. Click the Start button on the field PC, click Settings, and then the System tab.
       f. Click on the External GPS icon.
       g. Click on the Hardware tab and set the GPS hardware port = COM2
       h. Click ok to close window
       i. If you installed the GPSinfo utility, run it to check the GPS receiver
                 i. Click Start, click Programs, and then click the GPSinfo icon.
                ii. Set the port to COM2: USBSER, 4800 Baud
               iii. Click Start GPS
               iv. When done playing, click Close GPS and then close the application
3. GlobalSat/Trimble Bluetooth GPS
      a. Optional:
                 i. Run the GPS_Information.exe on your computer to install the GPSinfo utility on the
                    field PC.
      b. Turn on the GPS unit.
      c. Click the Start button on the field PC, click Settings, and then the Connections tab.
      d. Click “Add new device…”
      e. When listed, click on the GPS device (“BT-GPS-xxxxxx”), then click Next.
      f. When prompted, enter the pass code, then click Next.
                 i. GlobalSat = 0000
                ii. Trimble = 0183
      g. Click done when a connection has been made.
      h. Click “ok” to return to the Settings screen
      i. Click the System tab.
      j. Click on the External GPS icon.
      k. Click on the Hardware tab and set the GPS hardware port = COM2
      l. Click ok to close window
      m. If you installed the GPSinfo utility, run it to check the GPS receiver
                 i. Click Start, click Programs, and then click the GPSinfo icon.
                ii. Set the port to COM2: USBSER, 4800 Baud
               iii. Click Start GPS
               iv. When done playing, click Close GPS and then close the GPSinfo application
4. Ohaus ScoutPro USB Scale
      a. Plug in the USB cable to the field PC and power up the ScoutPro Scale.
      b. If not prompted for a driver name, do a soft reset of the field PC:
                 i. Hold the power button down for 5 seconds
                ii. Click the “Reset” button on the display
               iii. Wait for the field PC to complete the reset operation
      c. When prompted for the driver name, enter: ftdi_ser.dll

5. Destron Fearing 2001S-ISO RS232 Transceiver Settings:
      a. Create File = No
      b. User Profile #1 (will use this profile for PIT Tagging)
               a. Tag Type
               b. Antenna Power = 10% (for PIT Tagging)
               c. Store Mode = All
               d. Continuous Mode = On
               e. Toggle Mode = No
               f. Unique Mode = Off
               g. Shutdown Time = 5 mins
               h. Comm (N,8,1) Speed 9600
               i. Send Tag ID to CommPort = Form1
               j. Send Alarms to CommPort = On
               k. Antenna Led = Off
               l. Backlight Mode = Off
               m. Beep Sound = On
               n. Click Sound = On
               o. Decimal Tag = No
               p. Time Tag = Yes
      c. Connect the serial cable to the field PC.
      a. RS-232 Settings
                i. Bit rate 9600 baud
               ii. Data bits 8
              iii. Parity none
              iv. Flow control Off
      b. Display Setup
                i. Format HEX
               ii. Lead 0’s YES
              iii. Last Tag ON
              iv. City Code ALPHA
               v. F/H/A NO
      c. Reader Settings:
                i. Beep Setting EVERY
               ii. Autoread ON
              iii. Wrlssync OFF
              iv. Time On: 30:00 Min
               v. Read Time 3 Sec.
      d. ID Code Format:
                i. Format HEX
               ii. City Code ALPHA
              iii. Leading 0’s YES

                iv. Duplicates YES
                 v. Time Date OFF
                vi. RSRV FLD OFF
               vii. DB Flag OFF
              viii. C/M Code ON
                ix. Delimitr “.“
                 x. 1st char NONE
                xi. Tag-Type TI-RFID
7. Files and Folders:
       a. PIT Tag File Codes and Vials: the tag files must be copied to the exact folders on the field PC:
                  i. \QC_PITTag\QC_Tags\8_5mm\(tag files)
                 ii. \QC_PITTag\QC_Tags\12mm\(tag files)
                iii. Each tag file contains 100 tag identifiers, one per line. That tags must be in “HEX”
                iv. The tag file name is the “vial” that contains the tags.
                          1. Example: “CU11412.txt”
                 v. There is also a file in the \QC_PITTag\QC_Tags\ folder named “TagsUsed.csv”. This
                     is a log file that holds a record of every PIT Tag read by the reader.
       b. There are other files that must be transferred to the field PC or the application cannot work.
           The following is a list of files, folders, and a brief explanation of what each of the files is used
                  i. \QC_PITTag\QC_Input – this folder holds the files that are used for data lists and
                     range checking. These file will only be read, and need only be put on the field PC
                     one time, unless new list data is needed or different range values.
                          1. FieldSiteList.csv – this is a list of the sites that have been created in the field.
                               This file follows the same format as the SiteList.csv file.
                          2. ListData.csv – this file contains the lists of data that are used to populate the
                               controls that offer a selection of one or more items.
                          3. RangeList.csv – this file has the numeric ranges for the data types. Each
                               numeric value is compared against four limits:
                                    a. Minimum – a value below this is deemed bad (out of range)
                                    b. Expected Low – a value below this is a warning
                                    c. Expected Hi – a value above this is a warning
                                    d. Maximum – a value above this is deemed bad
                          4. SiteList.csv – this is the list of sites that are targeted for surveys. This is
                               generated in the “office”.
                          5. SpeciesCodesList.csv – this is an ordered list of species that provide the
                               selection list for captured fish.
                 ii. \QC_PITTag\QC_Config\Config.csv – this file contains some basic field PC
                          1. Data logger ID (A to H)
                          2. Use the GPS
                          3. Use the Tag Reader
                        4. Use the USB Scale
               iii. \QC_PITTag\QC_Sites – this folder contains each of the Dce’s. Each Dce will have a
                    folder that is the name of the Dce, and will contain the files that make up the
                        1. DataCollectionEventRecord.csv – this will hold one record (row) after the
                             header row that has the properties of the Dce as captured in the field.
                        2. FishCapturePasses.csv – this file will hold multiple records, one for each
                             capture pass with its corresponding data.
                        3. FishObservations.csv – this file will hold all the fish for each capture pass for
                             the Dce.
               iv. \QC_PITTag\QC_Recover – this is a duplicate copy of the …\QC_Sites\ folder for
                    emergency recovery only.
                v. \SD_Card\ - if a backup copy is selected at the end of the survey, and there is not a
                    d-micro flash card in the field PC, then a backup copy of the data will be made in this
8. Other Field PC Setup:
      a. Install a micro-SD memory card into the field PC – this is the backup storage for the
           application. The suggested size is 1 GB.
9. Operating Guidelines: how it works…sort of
      a. Launch the application by tapping the “QC_PITTagging” entry in the Start button menu.
      b. While the splash screen is displayed, the application is initializing internal data structures,
           reading the tag files, and reading the values from the files in the QC_Input folder.
      c. Main screen – Setup/SiteSelection:
                 i. Use the check boxes to select the
                    peripheral set that you will be using.
                ii. Note the ID in the top banner, above the
                    version number – it is very long and I am
                    working on a shorter version, but that is
                    what is being used this week.
               iii. There is displayed a count of the tags that
                    were read in from the QC_Tags
                    folder…three sizes.
               iv. The “New Site” button allows you to make a new site in the field.
                v. The “Edit Site” button allows you to make changes to an existing site (from the
                    SiteList.csv file). Changes are not saved back to that file, but are saved in the
                    FieldSiteList.csv file.
               vi. Select a site from the drop down list – note the stream name is displayed.
              vii. Lock the site to go to the next step, the “Data Collection Event” tab.
             viii. The “EXIT” button with do just that – it is not available until the site is unlocked.
      d. Data Collection Event Screen:
                 i. Select the name of the person making the changes to the Dce information.

                 ii. If you want to make a new Dce, select the start date and time for the Dce and then
                     click the “Make New Dce (Name)” button. This will make a Dce with a name made
                     from the site name and the start date that you entered before pressing the button.
                     Note: there can be only one Dce per day for a single site.
                iii. Select the Dce that you are going to survey by selecting its name in the Dce list.
                iv. If you need to delete an existing Dce, it must be selected and then you need to click
                     the “Remove Dce” button – you will then be prompted about your sanity and
                     allowed to proceed. This will remove the Dce from the QC_Sites folder, but will
                     leave the duplicate copy in the QC_Recovery folder.
                 v. With the Dce selected you can enter the length and width.
                vi. You must lock the Dce to move to the next step in the survey.
       e. Fish Capture Pass Screen:
                  i. Each capture pass must be done with a new “record” – add a record by clicking the
                     “Add Record” button.
                 ii. Select the capture pass record in the drop down list before proceeding to the next
                     screen for tagging and observation.
       f. Fish Observation Screen:
                  i. A new fish can be added in two ways:
                          1. Scanning a PIT Tag with the tag reader – this will also fill in the PIT Tag data
                                  a. PIT Tag ID
                                  b. PIT Tag Capture Type
                                  c. PIT Tag Type
                                  d. PIT Tag Vial Code
                          2. Clicking the “Add Fish” button – after you have added a fish, scanning a PIT
                              Tag will fill in the PIT Tag fields, as long as the “Will Tag” checkbox is
                              checked, and the “Lock Tag” checkbox is not checked.
                 ii. Enter the fork length
                iii. The weight is either entered manually if not using the USB scale, or once this text
                     box is selected, the USB scale will begin taking readings and calculating the weight
                     (see the section in “Other Stuff” for more information).
                iv. Check the “Lock” checkbox next to the weight field to lock in the current weight.
                 v. Fill in the other data as needed or specified in the protocol document.
                vi. When done with this fish, move on to the next one or go back to the previous
                     screen when done. Each time you move to a new fish, or change the screen with
                     the tab page control, the data on that screen is saved twice.
10. Other Stuff You Need To Know
       a. Tag Scanning:
                  i. Scanning a new tag will:
                          1. Over write the current PIT Tag identifier if the “Lock Tag” checkbox is

                 2. Make a new fish and assign this PIT Tag to the new fish if the lock tag
                     checkbox is checked.
        ii. If scanning a tag shows in the tag in the reader display, but the tag does not get sent
            to the data logger:
                 1. Verify connection of the serial cable to the data logger.
                 2. Navigate to the Setup tab and verify that the checkbox is checked
                 3. Uncheck the checkbox for using the tag reader, and then check it again –
                     this will re-initialize the serial port and should return the tag reader to
                     correct operation.
                 4. If this does not correct the problem, exit the application and restart it.
b. Scale Identification:
         i. If you want to use the auto advance feature, the identifier must end in a “whole” or
            integer number, such as:
                 1. AB-0012  AB-0013
                 2. 1200123  1200124
                 3. XYZ1A0011  XYZ1A0012
        ii. Don’t use a decimal in the number. Don’t use a comma in the number.
       iii. If you select Auto Advance Scale ID:
                 1. Checking the box will carry forward the scale sequence from the last scale
                 2. If the ID is not correct, edit it and it will advance this new ID on subsequent
                 3. If you uncheck the auto advance checkbox, it will use whatever ID you enter
                     and each fish will need you to enter a new ID.
       iv. If the scale stops working:
                 1. Navigate to the Setup tab and verify that the checkbox is checked for the
                     USB scale.
                 2. Uncheck the USB scale checkbox and then check it again – this will re-
                     initialize the communication port used for the scale and should return it to
                     normal operation.
                 3. If that does not work:
                          a. Uncheck the USB scale checkbox.
                          b. Disconnect the USB cable to the scale.
                          c. Power cycle the scale.
                          d. Connect the USB cable to the data logger.
                          e. Wait one minute (let the USB cable get discovered).
                          f. Check the USB scale checkbox.
c. Group Fish:
         i. You must un-check the Will PIT Tag checkbox for group fish – this will allow you to
            check the group fish checkbox and then fill in the size class and quantity

       d. Fish Weight:
                 i. To use the USB scale to enter fish weight, you must enable iton the first screen.
                ii. On the fish observation screen you must have the fish weight text box selected and
                    the lock fish weight checkbox unchecked. The weight will be sampled about 5 times
                    per second, the weight displayed will be the average of the three median values of
                    the last five readings (throw out the high and low and average the other three).
               iii. Check the lock weight box when you are satisfied with the reading.
NOTE: this algorithm is an experiment and will likely need to be modified based on field experience – invent
something better!


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