photo monitoring plug in guide

8/9/2019 Photo Monitoring Plug in Guide

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24 June 2014

Guide for using the Photo Monitoring Plugins

OverviewThis guide explains how to use the photo monitoring plugins written to work with ImageJ anda variant of ImageJ called Fiji. Since Fiji has most of the plugins accessed by the hoto!onitoring plugins bundled with the distribution it is easier to work with Fiji but the pluginsshould work e"ually as well in ImageJ if the installation instructions below are followed.

There are four plugins. Two are designed to create #$%I or $%I and false color images usingimage pairs ac"uired from two cameras. &ne of the dual'camera plugins creates a text file ofmatched image pairs ac"uired using two different cameras and another that uses the imagepair file and geometrically registers one of the images to overlay over the other and alsocalculates #$%I or $%I and related image products if one of the cameras records a near'infrared (#I)* image. The other two plugins are designed to create #$%I images from asingle camera with a filter that allows one waveband of visible light (usually blue or red* andalso near'infrared light to pass and be recored by the camera sensor. &ne of these single'camera plugins processes all of the images in a directory and the other processes an imagethat is displayed in ImageJ or Fiji.

+n attempt has been made to create some processing messages that will be output to theImageJ,Fiji - og/ window. 0hen an error occurs an informative message should be displayed.lease keep in mind that the plugins are still in a beta state so you should maintain a backupcopy of all of your images in case the input images are altered. Some troubleshooting topsare provided at the end of this document.

This guide and the plugins are works in progress and comments are welcome. I workprimarily with the 1buntu operating system so these instructions are based on my experiencewith 1buntu. If you notice something that should be altered to accommodate other operatingsystems please let me (#ed 2orning ' horning3amnh.org * know.

Installing the pluginsThe first step is to download and install ImageJ or Fiji (recommenced* which is a distributionof ImageJ 4 a powerful image processing package designed to support the biomedicalresearch community. Fiji can be downloaded from http5,,Fiji.sc,wiki,index.php,Fiji . It is Javabased and runs on all computers that support Java. +fter Fiji is installed you should launch it

then click on the menu -2elp 67 1pdate ImageJ/ to get the most recent version of the ij.jarfile. If the update does not work you can do the update manually by downloading the mostrecent version from here5 rsb.info.nih.gov,ij,upgrade,ij.jar. #ext8 replace the old ij.jar file thenew one in the -jars/ directory which is located under the Fiji root directory. 9ou must use aversion that is more recent than :.;..jar and xmpcore.jar files.

mailto:[email protected]://fiji.sc/wiki/index.php/Fijihttps://github.com/nedhorning/PhotoMonitoringPluginhttp://fiji.sc/wiki/index.php/Fijihttps://github.com/nedhorning/PhotoMonitoringPluginmailto:[email protected]


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+ copy of these files are available on the =it2ub site in the downloads directory or you canget it from5 http5,,code.google.com,p,metadata'extractor,downloads,list . 9ou need todownload the metadata'extractor'>..?ip file and then un?ip that file to get the metadata'extractor'>..jar and xmpcore.jar files.

9ou can install the plugins either by copying the -.jar/ files into the plugins directory which is

in the Fiji or ImageJ root directory or by dragging the file from your file browser onto the Fijimenu. If you drap the file to the Fiji menu a -Save lugin8 !acro or Script.../ window will openand you can click the -Save/ button to copy the plugins. 9 ou should now see a listing labeled- hoto!onitoring/ under the lugins menu. @licking on that will reveal the plugins describedin this guide. !ore information about installing plugins can be found here5http5,,fiji.sc,wiki,index.php,InstallingABrdApartyAplugins.

If the plugins are used with ImageJ then the following additional .jar files from the Fiji projectneed to be also copied to the plugins directory5 jars,mpicbg.jar8 plugins,mpicbgA.jar8 andplugins,b1nwarpJA.jar. +lso8 the metadata'extractor'>..jar and xmpcore.jar files must becopied to the plugins directory.

Using and creating custom lookup tables + lookup table ( 1T* is used to define which colors will be used to represent different #$%Ivalues when a color #$%I image is output. ImageJ and Fiji have several do?en 1Ts butnone dedicated specifically for #$%I. + set of 1Ts have been created to render #$%I imagesin color. The custom 1Ts can be found on the =it2ub site5https5,,github.com,nedhorning, hoto!onitoring lugin . The human readable @S% files used tocreate the 1Ts using the ImageJ - 1T Importer/ plugin ( http5,,rsbweb.nih.gov,ij,plugins,lut'importer.html * are located in the main =it2ub page and the binary 1Ts for direct use withImageJ or Fiji are in the downloads directory.

To install the 1T you need to copy the .lut file (from the downloads directory of the =it2ubsite* to the -luts/ directory which is in the Fiji or ImageJ root directory. The next time you startImageJ or Fiji the 1T should appear in the list of 1Ts. To see what the 1T looks like youcan use a ImageJ,Fiji utility. =o to Image 67 ookup Tables then click on the 1T youCd like tosee and a color bar will open. The color on the left side of the bar represents an #$%I valueof D and the color on the right side represents a value of >EE.

If you want to create your own 1T you need to create a @S% file with the first columncontaining the pixels value (D to >EE* and the next three columns are the intensity values for)ed8 =reen8 and lue respectively. + @S% file can be created using a spreadsheet such as

Gxcel or @alc. The lowest valid value for these three columns is D and the highest is >EE. 9oucan use the @S% file in the =it2ub site as an example. &nce the @S% file is finished you needto use the - 1T Importer/ plugin to convert the values to a format that can be used byImageJ,Fiji. +fter running the - 1T Importer/ plugin with the color bar displayed and activeyou can save the 1T by clicking on Image 67 @olor 67 Gdit 1T... then when the 1T Gditoropens click save. Save the 1T in the -luts/ directory which is in the Fiji or ImageJ rootdirectory. The 1T will appear in the list of 1Ts next time you open ImageJ,Fiji.

2ere is a brief description of the different custom 1Ts5

http://code.google.com/p/metadata-extractor/downloads/listhttps://github.com/nedhorning/PhotoMonitoringPluginhttp://rsbweb.nih.gov/ij/plugins/lut-importer.htmlhttp://rsbweb.nih.gov/ij/plugins/lut-importer.htmlhttp://code.google.com/p/metadata-extractor/downloads/listhttps://github.com/nedhorning/PhotoMonitoringPluginhttp://rsbweb.nih.gov/ij/plugins/lut-importer.htmlhttp://rsbweb.nih.gov/ij/plugins/lut-importer.html


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• ndviClasses_0_1.lut: :: different colors ranging from reddish brown for low #$%I todark green for high #$%I. This is designed to work with scaling #$%I values from D to:.

• ndviClasses_-1_1.lut: :: different colors ranging from reddish brown for low #$%I todark green for high #$%I. This is designed to work with scaling #$%I values from ': to:.

•

ndviClassesCB_0_1.lut: $esigned for people with color blindness. It has :: differentcolors ranging from purple for low #$%I to dark green for high #$%I. This is designedto work with scaling #$%I values from D to :.

• ndviClassesCB_-1_1.lut: $esigned for people with color blindness. It has :: differentcolors ranging from purple for low #$%I to dark green for high #$%I. This is designedto work with scaling #$%I values from ': to :.

• colorRampNDVI.lut: + gradient from light beige for low #$%I to very dark green forhigh #$%I. This will work with scaling ranging from ': to : and D to : but the results willbe very different.

• NDVIBlue2Red.lut: + gradient from blue to red.• NDVIBlue2RedWB: TSimilar to the #$%I lue>)ed but color pixels with a value of D to

white and pixels with a value of >EE to black.

Remove low quality photosefore you use the plugins itCs a good idea to review your photos and remove any that are oflow "uality or have no image on them. The current version of the plugin is known to free?ewhen an all black image (like one you would get if you had the lens cap on* is encountered.

Plugin to create file of image pairsThe -@reate dual image list/ plugin is designed to facilitate the process of matching two digitalphotographs that were ac"uired at roughly the same time. The plugin outputs a text file withthe path and file names for image pairs (e.g.8 images ac"uired from two cameras* that can beinput into the -)eg images/ plugin. The image matching is done by synchroni?ing the timesstored in the image GHIF $ateTime&riginal tag from each of two cameras. If for some reasonthe GHIF $ateTime&riginal tag is not set then the files last modified time will be used.

efore running the plugin the images from each camera should be stored in differentdirectories. If this is not convenient please let me know of your preferred method fordifferentiating between the images ac"uired from each camera and I will consider addingalternative methods.

Synchroni?ation of the image pairs is done by calculating or reading a user defined offsetbetween the imaging time recorded by one camera with the image time from another cameraand then using the offset to find which images were ac"uired at roughly the same time.

0hen the plugin starts a dialog window is opened with the following options5

Select offset calculation met od: There are three options for calculating the time5• Assume already synched: +ssumes the camera clocks were synchroni?ed to the same

time before photo were ac"uired so an offset of D seconds will be used.• Enter offset: +llows you to enter the offset in seconds. The offset should be calculated


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using this e"uation5 time of visible image 4 time of #I) image. It the result is negative itis important to include the negative sign (-'/* before the number of seconds.

• Calculate offset from pair: 1ses two images from a pair (one visible one #I)* tocalculate the offset. If this option is selected then you will have to specify the visibleand #I) images that were ac"uired at the same time and will be used as the referencepair.

Max difference in seconds between offset-corrected image pairs: This is the maximum timedifference in seconds8 after the calibration has been applied8 that is allowable between eachimage pair. This compensates for slight variations in the camera clock and shutter releasemechanism.

If the -Gnter offset/ option is selected you will need to enter the offset (calculated as5 time ofvisible image 4 time of #I) image* in seconds.

If the -+ssume synched/ or -Gnter offset/ options are selected you will need to select thelocation for the visible and #I) images.


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If the -@alculate from pair/ option is selected then you will need to select the visible image thatwill be used as a reference to synchroni?e the times to select image pairs. +fter clicking -& /a window will open so you can select the #I) image that will be used as a reference. For both

of these windows the assumption is made that all of the visible images that will be processedare in the same directory as the visible reference image and all of the #I) images are in thesame directory as the #I) reference image.

)egardless of the other options the last window is where you select the output file locationand name. +fter selecting the directory path and entering the output file name click on -Save/to run the program. It should complete in seconds.


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Image registration and index image pluginThe -$ual image index processing/ plugin is designed to co'register two images8 one using a#I) camera and the other a -normal/ visible camera. The plugin will work best if the imageswere ac"uired from two cameras mounted with their lenses close to each other8 ac"uired atnearly the same time (so the scene hasnCt changed*8 and itCs best if the two cameras havesimilar characteristics such as image si?e and resolution.

The plugin can output the following images5#)= image (false'color image with )6#I)8 =6red from visible8 and 6green from visible*#$%I or $%I image with a user'selected color table appliedFloating point #$%I or $%I image with actual #$%I values (data range ': to : for #$%I or'>EE to >EE for $%I*

+ visible image clipped to the common area between the registered #I) and visible image + log file documenting the registration method used for each image pair

The parameters used to run SIFT8 andmark correspondences8 and b1nwarpJ are coded intothe plugin and at this point can not (at this time* be modified by the parameter windowdisplayed by this plugin.

Instructions

efore running the plugin you will need to prepare a text file that directs the plugin to processspecific image pairs. This can be accomplished by running the -@reate dual image list/ plugindescribed above or by creating your own file.

If you create your own file you need to ensure the following format is followed. Gach line in thefile must have the directory path and file name for the two images that form a pair with acomma separating the two. The first image is the nearAI) image (the source image that will

be warped* and the second image is the visible image (the target image used as a referencebut not altered*. !ake sure there is no whitespace (space8 tab8 or new line* after the last lineof text.2ere is an example of what the text file looks like for two image paris (; images*5ned,InputImages,nir, %'DDD:.J =8 ned,InputImages,visible, %':B>;.J =ned,InputImages,nir, %'DDDB.J =8 ned,InputImages,visible, %':B>E.J =

The plugin will work with any image format that can be read by ImageJ,Fiji. 9our first (test* runshould probably include just a couple image pairs to make sure itCs working.

To run the plugin go to lugins 67 hoto !onitoring 67 $ual image index processing. 0hen

the plugin starts a dialog window opens that lets you specify processing options.


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!odify the following options to specify the output that you want to create.• !oad default parameters: If you check this checkbox and then click on the -& /

button at the bottom of the window the default parameters will be entered. This ishelpful if you modify some of the parameters and forget what the default settings were.

• "se #ac$up re%istration met od if primar& fails: This option allow you to specify ifyou want to try a backup registration method if the primary method fails.

• Select primar& re%istration met od: This is the first registration method that will betried for the image pair. Three registration methods are available. The first8-SIFT, andmark correspondences/8 uses a scale'invariant feature transform (SIFT* toselect matching points in image pairs. +fter points are selected a transformation is

applied that will modify the #I) image. 1nfortunately SIFT often does not always selectpoints that correspond with both images in landscape photos since there are ofter notenough distinct features that can be detected and match. + second registration option8-SIFT, andmark correspondences using reference points from first valid image pair/will use the reference points from the previous set of correspondence points calculatedusing SIFT. This option is fast since new correspondence point do not need to becalculated but the results will only be good if there is no relative movement betweenthe two cameras that ac"uired the image pairs. The third option is -b1nwarpJ/ whichuses the b1nwarpJ plugin in Fiji. This algorithm is able to register most image pairs


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and is able to deal with more severe types of image mismatches. The downside is thatthis algorithm take more time (K; minutes vs :E seconds for the SIFT approach* and itcan introduce distortions if the corresponding reference points in the image pair are notvery accurate and well distributed throughout the image. !ore information aboutb1nwarpJ can be found at http5,,biocomp.cnb.uam.es,Kiarganda,b1nwarpJ, .

• Select secondar& re%istration met od: These options8 similar to the primary

registration options described above8 are applied if a backup registration method isre"uested using the checkbox at the top of the parameter window.• Select transformation t&pe if usin% SI'(: The transformation type option only has an

effect if you use the SIFT registration method selected. The affine transformationadjusts the image using translation8 rotation and scaling and the rigid transformationonly uses translation and rotation. The rigid transformation sometimes produces abetter image'to'image fit when few corresponding points are selected using SIFT.

• Num#er of tries for SI'( to find correspondence points 5 This specifies the numberof times the SIFT algorithm will run to find corresponding reference points on the twoimages. The results differ each time the SITF algorithm runs so for difficult to matchimage pairs running multiple time will sometime result in a match. If you do not want to

use multiple runs set this to -:/.• )et od to improve point selection: This option presents different pre'processing

methods that can be used to improve the ability of the SIFT algorithm to findcorresponding points. This is experimental and the only option at this time is Ltarget (g'b* source (g b*L which subtracts the blue channel from the green channel of the target(visible* image and adds the green channel to the blue channel of the source (#I)*image to create input images for the SIFT algorithm. This approach seems to work wellfor the camera pairs made using the information on the &TS web site. &therapproaches can be added for camera pairs if this algorithm isnCt effective.

• ele!t inde" t#$e for !%l!ul%tion: This dropdown menu lets you choose the type ofindex you want to create (e.g.8 #$%I or $%I*.

•

*utput ima%e t&pe: File format for the output images. )emember that if you want tooutput a floating point #$%I image you will need to select an image format thatsupports floatig point numbers such as TIFF. !ost common graphics image formatssuch as J G= do not support floating point numbers and will cause the output image toappear black.

• *utput NR+ ima%e,: &utput a false'color composite image with the following )=color channel assignments5 )6#I)8 =6red from visible8 and 6green from visible.

• &li$ i'%ges(: @lip the images so that only the common area dimensions are used inthe output images. In most cases this is desirable but if you needed to have all of theoutput images to maintain their original dimensions you would want to un'check thisbox.

• *utput clipped visi#le ima%e,: If -@lip images/ is checked then output a copy of thevisible image that is clipped to match the dimensions of the other output images.

• *utput &olor inde" i'%ge(: &utput a color #$%I image using the look'up tablespecified below.

• Mini'u' inde" )%lue for s!%ling !olor inde" i'%ges: 0hen the color index imageis created it is necessary to scale from actual floating point #$%I values (possiblevalues range from ':.D to :.D for #$%I and '>EE to >EE for $%I* to a range of integers(possible values range from D to >EE* allowed for the color image. This parameterallows you to set the minimum index value that will be assigned to a value of D in the

http://biocomp.cnb.uam.es/~iarganda/bUnwarpJ/http://biocomp.cnb.uam.es/~iarganda/bUnwarpJ/


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output color image. #$%I values between the minimum and maximum (nextparameter* are scaled linearly from D to >EE.

• M%"i'u' inde" )%lue for s!%ling !olor inde" i'%ges: Same principle as theprevious variable but value you enter here will be assigned to a value of >EE in theoutput color image.

• *utput floatin% point inde ima%e,: &utput a floating point index image with actual

values 4 not scaled from D to >EE.• tret!h the )isi*le *%nd *efore !re%ting inde"(: This option will stretch the visible

band used to calculate #$%I. This can be used to normali?e images if the features ineach image are similar. If some images are mostly vegetation and some are mostlyurban environments using this techni"ue to normali?e images might not work well.

• tret!h the NIR *%nd *efore !re%ting inde"(: Similar to the previous parameter butfor the #I) band used to calculate #$%I.

• %tur%tion )%lue for stret!h: The saturation value determines a threshold for extremevalues in the image. In other words it defines which of the lowest values will be set to Dand which of the highest values will be set to >EE. If the default value of >.D is usedthen : percent of the lowest values will be set to ?ero and : percent of the highest

values will be set to >EE and the remaining values will be linearly scaled to a range of Dto >EE.

• C annel from visi#le ima%e to use for Red #and to create inde : Select thechannel number from the visible image that will be used as the red band in the #$%Iformula. The default selection seems to work well with most color digital cameras.

• C annel from IR ima%e to use for NIR #and to create inde : Select the channelnumber from the near'infrared image that will be used as the #I) band in the #$%Iformula. The default selection seems to work well with the &Ts nearI) cameras.

• Select output color ta#le for color inde ima%e: The color lookup table to be used ifa color #$%I image is being output. 9ou can add new color lookup tables to Fiji,ImageJby following the instructions in the ImageJ manual.

• %)e $%r%'eters for ne"t session: Save the parameters entered in this window anddisplayed them the next time the plugin is run.

+fter you select the options you want click on -& /. The next window allows you to select thefile containing the path and image names of each image pair is located. Select the file(possibly the output from the @reate list plugin* and click -& /.


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The last window allows you to select the directory where the images and log file will beoutput. 9ou can also change the name of the log file that is output when the plugin is run. Thelog file will be output to the same directory as the output images. +fter you specifying thedirectory and log file click on -Save/ to start processing.

If the SIFT registration method is selected and an image pair fails to register after E tries thatpair will be skipped and processing of the remaining image pairs will continue.


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Index images from a directory of images pluginThe -Single image index from directory/ plugin is designed to create color and floating pointindex images from a directory containing images that recorded visible light in one band andnear'infrared light in another. These images can be captured using the Super lue filteravailable from ife ixel (http5,,www.lifepixel.com,* or from ublic abs5(http5,,www.kickstarter.com,projects,publiclab,infragram'the'infrared'photography'project*.The plugin processing images faster than the dual'camera images since no image warping isnecessary.

Instructions

efore running the plugin you will need to ensure that all of the images that you want toprocess are in a single directory with no other files. To run the plugin go to lugins 67 hoto!onitoring 67Single image #$%I from directory. 0hen the plugin starts a dialog windowopens that lets you specify processing options.


button at the bottom of the window the default parameters will be entered. This is


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helpful if you modify some of the parameters and forget what the default settings were.• ele!t inde" t#$e for !%l!ul%tion: This dropdown menu lets you choose the type of

index you want to create (e.g.8 #$%I or $%I*.• *utput ima%e t&pe: File format for the output images. )emember that if you want to

output a floating point #$%I image you will need to select an image format thatsupports floatig point numbers such as TIFF. !ost common graphics image formats

such as J G= do not support floating point numbers and will cause the output image toappear black.• *utput &olor inde" i'%ge(: &utput a color #$%I image using the look'up table

specified below.• Mini'u' inde" )%lue for s!%ling !olor inde" i'%ges: 0hen the color index image

is created it is necessary to scale from actual floating point #$%I values (possiblevalues range from ':.D to :.D for #$%I and '>EE to >EE for $%I* to a range of integers(possible values range from D to >EE* allowed for the color image. This parameterallows you to set the minimum index value that will be assigned to a value of D in theoutput color image. #$%I values between the minimum and maximum (nextparameter* are scaled linearly from D to >EE.

•

M%"i'u' inde" )%lue for s!%ling !olor inde" i'%ges: Same principle as theprevious variable but value you enter here will be assigned to a value of >EE in theoutput color image.

• *utput floatin% point inde ima%e,: &utput a floating point #$%I image with actual#$%I values that range from ': to :.

• tret!h the )isi*le *%nd *efore !re%ting inde"(: This option will stretch the visibleband used to calculate #$%I. This can be used to normali?e images if the features ineach image are similar. If some images are mostly vegetation and some are mostlyurban environments using this techni"ue to normali?e images might not work well.


• %tur%tion )%lue for stret!h: The saturation value determines a threshold for extremevalues in the image. In other words it defines which of the lowest values will be set to Dand which of the highest values will be set to >EE. If the default value of >.D is usedthen : percent of the lowest values will be set to ?ero and : percent of the highestvalues will be set to >EE and the remaining values will be linearly scaled to a range of Dto >EE.





+fter you select the options you want click on -& /. The next window allows you to select thedirectory with the input images and click -& /.


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The nextwindow allows you to select the directory for the output images and the name of the log filecontaining all of your parameter settings. @lick -& / after selecting the directory.

+fter selecting the output directory and log file name the images will be opened one'by'oneand processed.


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N !I from an opened image pluginThe LSingle image #$%I from displayed imageL plugin is designed to create color and floatingpoint #$%I images from an image displayed in ImageJ,Fiji that recorded visible light in oneband and near'infrared light in another. These images can be captured using the Super luefilter available from ife ixel (http5,,www.lifepixel.com,* or from ublic abs5(http5,,www.kickstarter.com,projects,publiclab,infragram'the'infrared'photography'project*.The plugin processing images faster than the dual'camera images since no image warping isnecessary. This plugin displays the output images on the screen but does not save them todisk. If you want to save the images you can do so using the ImageJ,Fiji save feature.

Instructions

efore running the plugin you will need to ensure that all of the images that you want toprocess are in a single directory with no other files. To run the plugin go to lugins 67 hoto!onitoring 67Single image #$%I from displayed image. 0hen the plugin starts a dialogwindow opens that lets you specify processing options.


button at the bottom of the window the default parameters will be entered. This ishelpful if you modify some of the parameters and forget what the default settings were.

• ele!t inde" t#$e for !%l!ul%tion: This dropdown menu lets you choose the type of


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index you want to create (e.g.8 #$%I or $%I*.• Displa& &olor inde" i'%ge(: &utput a color #$%I image using the look'up table

specified below.• Mini'u' inde" )%lue for s!%ling !olor inde" i'%ges: 0hen the color index image

is created it is necessary to scale from actual floating point #$%I values (possiblevalues range from ':.D to :.D for #$%I and '>EE to >EE for $%I* to a range of integers

(possible values range from D to >EE* allowed for the color image. This parameterallows you to set the minimum index value that will be assigned to a value of D in theoutput color image. #$%I values between the minimum and maximum (nextparameter* are scaled linearly from D to >EE.

• M%"i'u' inde" )%lue for s!%ling !olor inde" i'%ges: Same principle as theprevious variable but value you enter here will be assigned to a value of >EE in theoutput color image.

• Displa& floatin% point inde ima%e,: &utput a floating point #$%I image with actual#$%I values that range from ': to :.

• tret!h the )isi*le *%nd *efore !re%ting inde"(: This option will stretch the visibleband used to calculate #$%I. This can be used to normali?e images if the features in

each image are similar. If some images are mostly vegetation and some are mostlyurban environments using this techni"ue to normali?e images might not work well.


• %tur%tion )%lue for stret!h: The saturation value determines a threshold for extremevalues in the image. In other words it defines which of the lowest values will be set to Dand which of the highest values will be set to >EE. If the default value of >.D is usedthen : percent of the lowest values will be set to ?ero and : percent of the highestvalues will be set to >EE and the remaining values will be linearly scaled to a range of Dto >EE.





+fter you select the options you want click on -& / and the image will be processed with theresults displayed on the screen.

"rror messages2ere are a few error messages and the recommended solutions. If you are not able to fix yourerror with this information please contact #ed 2orning ( horning3amnh.org *.

+rror:

mailto:[email protected]:[email protected]


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first line of the exception message is5 java.lang.#oSuch!ethodGrror5 ij.process.@olor rocessor.get@hannel(I*M

+"$l%n%tion %nd solution:9ou are using a version of ij.jar that is older than :.;..jarfile is in the Fiji -jars/ directory as explained in the -Installing the lugins/ sections above.

+nother possible reason for this error is that there is a conflict with another plugin that usessome of the classes in the metadata'extractor'>..jar file. There is an ImageJ plugin calledGxifA)eader installed that has some of the same of the metadata'extractor classes in its jarfile and this can cause a conflict with the photo monitoring plugins. To fix this problem you willneed to remove the GxifA)eader.jar file from the -plugins/ directory.

4

+rror:0hen running the -$ual image #$%I processing/ plugin a small window with the number -:/is displayed after entering the location of the log and output files. @licking on -& / closes thewindow and processing continues just fine.

+"$l%n%tion %nd solution:This will happen if there is one or more blank lines after the last line of text in the pairedimage file. To prevent this from happening be sure to remove all white space after the last lineof text in the paired image file. If this file is created using the -@reate dual image list/ pluginthis error should not occur.

photo monitoring plug in guide

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