PhilaJ: Philatelic Tools For ImageJ

Installing PhilaJ requires the "imagej/PhilaJ-and-RPI_Tools/PhilaJ.ijm" file in the PhilaJ distribution be copied into the Fiji toolsets directory. This directory is normally named "macros/toolsets/", and may be found inside the Fiji install directory. For example, I install Fiji at "c:\Users\richmit\PF\Fiji.app", and thus I copy the "PhilaJ.ijm" file to "c:\Users\richmit\PF\Fiji.app\macros\toolsets\PhilaJ.ijm".

If ImageJ was running when you copied the file, then you need to quite and restart it.

PhilaJ uses several "dot" files to customize and extended behavior. In the distribution you will find a directory called "dot-philaj" which contains the set of customization files I use. If you are just starting out, then you can start with these files. Copy them into the PhilaJ Configuration Directory.

ImageJ's default measurement settings are not ideal for PhilaJ, so we need to change those defaults. Select "Analyze -> Set Measurements" from the main ImageJ menu:

The following dialog box will appear:

It is important to select the three highlighted options:

• Area
• Bounding rectangle
• Display label

You can select others options as desired.

Why are these options important?

• Area: This one is used for centering, design, and paper measurements.
• Bounding rectangle: This one is used by most tools. It identifies the location and size of an ROI.
• Display label: PhilaJ frequently adds multiple measurements to the results window, and without labels they aren't very useful.

• —
• Remove/Reset Overlay
• Overlay/ROI Measure
• —
• Dynamic Perforation Gauge
• Dynamic Perforation Gauge Options
• Dynamic Perforation Gauge Presets
• —
• Instanta-Style Perforation Gauge
• Instanta-Style Perforation Gauge Options
• —
• Specialized Perforation Gauge
• Specialized Perforation Gauge Options
• Single Line Specialized Perforation Gauge Options
• Single Line Specialized Perforation Gauge Presets
• Install New Specialized Gauge
• —
• Position Finder
• Position Finder Options
• —
• Coordinate Tool
• Coordinate Tool Options
• —
• Grill
• Grill Type & Options
• Grill Options

The PhilaJ Overlay Interaction Tool allows a user to manipulate overlays created by the previous menu. For example, the Instanta-Style Perforation Gauge and Specialized Perforation Gauge may be moved around over an image in order to align them with a stamp's perforations. Some overlays, like the Dynamic Perforation Gauge, may be manipulated in more complex ways. Non-PhilaJ overlays can be moved around with this tool.

This toolbar button has a super power – Right click on it to bring up the primary options dialog for the currently active PhilaJ overlay.

• —
• Set scale for DPI: 2410x2398 – This odd DPI is what I get at the center of the platen on my Epson scanner. ;)
• Set scale for DPI: 2400
• Set scale for DPI: 1200
• Set scale for DPI: 600
• Set scale for DPI: 300
• —
• Set scale for DPI
• Set Scale for Hoiz & Vert DPI
• Set scale from DPI file name
• —
• Set scale from scale ROI
• Create scale ROI and add it to the ROI manager
• —
• Set Scale via standard ImageJ dialog
• Set Scale 1D
• Set Scale 1D from measurement results table
• Set Scale 2D
• Set Scale 2D from measurement results table
• Set Scale for Stereo Microscope Photograph
• —
• Convert image scale units to mm
• Shrink image to make pixels square
• Resize image to target DPI
• —
• Remove Scale
• Scale Report

• —
• Configure RPI Microscope Camera
• Live Video From RPI Microscope Camera (no capture)
• Capture Image From RPI Microscope Camera
• Load Previous RPI Microscope Camera Captures
• —
• Load ROIs from PhilaJ sidecar file
• Save ROIs to PhilaJ ROI sidecar file
• —
• Load Notes from PhilaJ sidecar file
• —
• Load image & ROI sidecar. Attempt to set Scale.
• Save image & ROI sidecar
• SaveAs image & ROI sidecar
• —
• Save Image As PNG
• Load Image
• —
• Delete current image file
• Delete current image file & close image window
• Delete current image file & close associated windows
• —
• Close PhilaJ Windows
• Close PhilaJ & Related Windows
• Close Image, PhilaJ, & Related Windows
• —
• Process a single scan
• Process a directory of scans
• Selection to image (with scale)
• Selection to JPEG
• Create Preview & Thumbnail Images
• Stamp Crop w/ Previous Settings
• Stamp Crop w/ New Settings
• Create ROI Annotated Image

• —
• ROI Manager...
• Bulk ROI Rename
• Clean up ROI list
• Delete centering report ROIs
• Create Special Stamp ROI
• —
• Measure Design
• Measure Paper
• Centering Report
• Coil Edge Check
• Measure Dynamic Perf ROI
• Measure ALL Dynamic Perf ROIs
• —
• Angle & Distance Between Edges
• Offset Between ROIs
• Create grill box ROI from grill points ROI
• —
• Rotate Line to Horizontal
• Rotate 90 Degrees Right
• —
• Separate stamp multiple
• Make Design ROIs for Multiple
• —
• Convert Distance to Perforation Measurement
• Convert Kiusalas to Perforations per 2cm
• Convert Perforations per 2cm to Kiusalas
• Convert length to millimeters
• —
• Kiusalas Table
• Grill Table
• —
• Measure Color
• Compare Two Colors

The dynamic perforation gauge is a fully interactive, digital perforation gauge capable of making very precise measurements of both perforations and hole size. With physical perforation gauges one finds the gauge row that most closely matches the perforation holes. The dynamic gauge only has one row of perforation dots, and the user adjusts the location (and optionally size) of these dots to match the perforation holes. The dynamic perforation gauge is started by selecting one of the following menu items in the overlay menu: Dynamic Perforation Gauge, Dynamic Perforation Gauge Options, or Dynamic Perforation Gauge Presets.

When using the Dynamic Perforation Gauge Options menu item, the dialog below will appear before the perforation gauge overlay is drawn.

When using the Dynamic Perforation Gauge Presets menu item, the dialog below will appear. These presets will set the initial hole size & spacing. Immediately after the preset dialog, the options dialog will be displayed just as if the Dynamic Perforation Gauge Options had been used.

The initial placement of the overlay may be controlled by an active line ROI when Dynamic Perforation Gauge or Dynamic Perforation Gauge Options is used – but not Dynamic Perforation Gauge Presets.

• If a line ROI was active when the menu option was selected, then the gauge will appear on the line
• If a line ROI is one previously created by the dynamic perforation gauge, then the number of perforation holes and perforation hole size may be automatically set.
• If no ROI is selected, then the gauge appears with the first dot in the upper left of the image and extending to the right

Once the gauge is displayed, it may be dynamically adjusted onscreen. While being adjusted a live perforation measurement may displayed. This live measurement may be presented in one of two ways: 1) graphically over the image itself, or 2) in a popup window.

• Click and drag any perforation gauge dot to move the dot around. Note that the end dot furthest away from the one you clicked on stays put while all the other dots follow your mouse around. The typical procedure is to drag an end dot to the first hole on the stamp, and then drag a dot on the other end of the perforation gauge to a hole on the other side of the stamp.
• If the HUD perforation report is being displayed, clicking on the HUD will allow you to drag just the HUD around. This is useful when the HUD is placed over a cluttered part o the stamp making the HUD hard to read.
• Clicking outside of the HUD and any perforation allows you to drag the entire perforation gauge line around on the display. This can be useful if you have just measured perfs on one edge, and wish to measure the other edge.
• Shift-Click outside of any perforation and drag to resize the perforation gauge holes. Moving away from the gauge makes the holes larger, and moving toward the gauge makes them smaller. The rate of change as you drag is slowed down to make precise chances possible, but this means that if large changes need to be made to the size you might have to repeat the procedure.
• Dots can be added or removed with an Alt-Click
  • Alt-Click on a dot, and all the dots left/right of that dot will be removed to the closet gauge end.
  • Alt-Click outside of any dot, and all a new dot will be added to the end of the gauge closet to the clicked point
  • The number of dots may also be added by bringing up the options dialog, and changing the value in the dialog. When changed in this manner, the end dots stay put and the gauge is redrawn.
• Control-click to get a perforation report or use the Overlay/ROI Measure command

In summary:

Once the gauge is adjusted to align with the stamp's perforation holes, a detailed perforation report may be generated via the Overlay/ROI Measure menu selection or by pressing the [M] key – note that is an upper case "M".

The report will be in a popup (just like the live measurement popup) if the option "Results in measure table" is not selected, otherwise it will be in the ImageJ measurement results window. If the "ROI Manager Use" option is set to anything other than "NONE", then ROIs describing the perforation gauge will be saved in ROI manager for later recall – see the section Reusing Dynamic Perforation Gauge ROIs.

ROIs created by the Dynamic Perforation Gauge can be used in a few different ways. Most directly, if one is active when the Dynamic Perforation Gauge menu is selected, then the Dynamic Perforation Gauge will startup with matching perforation spacing, hole count, and hole size. At this point the perforations can be remeasured, or the gauge may be adjusted.

The Convert Distance to Perforation Measurement menu item will also create a perforation report if a Dynamic Perforation Gauge line ROI is active when the menu is selected. In this case a dialog will appear allowing the user to manually adjust the numbers before the report is generated.

To simply remeasure the perfs, the Measure Dynamic Perf ROI item is the way to go. To generate a summary report for every Dynamic Perforation Gauge ROI in the ROI Manager, use the Measure ALL Dynamic Perf ROIs menu item.

The "static" perforation gauges are just like the physical perforation gauges we use. They work just like physical perforation gauges too. That is to say, one activates the gauges and then moves it around to line up the gauge on the perforations to be measured. In PhilaJ they come in two varieties:

• "Instanta-Style" – Continuous lines graduated with perforation measurements
• "Specialist-Style" – rows of dots like the Kiusalas gauges

These tools are found in the overlay menu. Instanta-Style Perforation Gauge & Specialized Perforation Gauge will draw the gauge immediately using the most recent, or default, settings. If you wish to change settings first, then the Instanta-Style Perforation Gauge Options & Specialized Perforation Gauge Options menu items will pop up a settings dialog before drawing the overlay.

One "moves" the gauge around via the PhilaJ Overlay Interaction Tool – the button just to the right of the overlay menu button. Simply click and drag while the PhilaJ Overlay Interaction Tool is active to move the gauge around.

Note that the stamp perforations must be perfectly lined up on a horizontal line to use these gauges! To do that, draw a line along the tops/bottoms of the perf holes, and then use the Rotate Line to Horizontal tool – in the misc menu or via the keybinding [1]. After you have measured the horizontal perforations and wish to measure the vertical ones, rotate the image 90 degrees via the Rotate 90 Degrees Right tool – in the misc menu or via the keybinding [2].

Unlike physical gauges, these gauges can be customized in various ways. First the graphical presentation (colors, line widths, etc…) can all be customized to make them more readable. Secondly, they can be customized geometrically as well. The Instanta-Style gauges can have the overall range adjusted and the graduations (1/10, 1/4, 1/2) adjusted. Note that by reducing the range one can obtain very accurate measurements with the Instanta-Style gauge.

The specialist-style options dialog provides a drop down of several gauges (Kiusalas, traditional Kiusalas, Bari Wolf, etc…). The end user can add to this list by saving CSV files describing new gauges (see: Install New Specialized Gauge).

If you just need a custom one row specialist-style gauge, then you can use the single line specialist gauge. It allows the user to specify the perforation frequency and perf sizes in a popup dialog. It automatically converts various measures for frequency and dot size so you don't have to use millimeters. I use this sometimes when working with a pile of stamps that need to be divided into two perforation groups – i.e. a stamp fits the gauge or doesn't. This gauge is available via the Single Line Specialized Perforation Gauge Options & Single Line Specialized Perforation Gauge Presets menu options.

Then menu option Install New Specialized Gauge in the overlay menu allows one to install new specialized gauges.

New gauges are described via a CSV file – which you can make with a text editor or Excel. These files contain three columns:

• Gaps – the center to center distance between perf holes (in millimeters)
• Hole Sizes – the diameter of the hole (in millimeters)
• Preset – If "Y" then the line will be included presets for the one line specialized gauges and the dynamic perforation gauge.
• Labels – a bit of text to identify each row of perforations

Here is an example of a custom gauge for the Bari Wolf issue (this file shipps with PhilaJ):

# Bari Wolf Issue Perforation Gauge
#
# Based upon measurements of my personal collection
#
# Hole to hole distance (gap) formula:
#            gap=20/perf     -- (perf units: holes per 2cm)
#            gap=mils*0.0254 -- (mils units: thousandths of an inch)
#
#         Gap,Hole,P,Label
1.84162062615,0.93,Y,10.86
1.83823529412,1.02,Y,10.88
1.81818181818,1.06,Y,11.00
1.74978127734,1.06,Y,11.43
1.74672489083,1.06,Y,11.45

The CSV files live in the "perfs" folder inside your PhilaJ configuration file directory.

The Install New Specialized Gauge menu option simply queries the user for a CSV file name, an copies it into the PhilaJ Configuration Directory. You don't need to use the Install New Specialized Gauge menu option – you can copy them in via the command line or a file explorer-like tool if you wish. All that matters is that they are in the correct place. Once they are installed, the new gauges will show up in the specialized perforation options dialog – no need to restart ImageJ.

Note the filenames are used much like ImageJ macro files. For example, a file named "AM_Post_BEP.csv" will result in a menu option named "AM Post BEP" – i.e. the underscores are turned into spaces and the extension is removed.

See the section Available Specialist gauges and presets for more information regarding gauges shipped with PhilaJ.

PhilaJ can be used to make various centering & paper measurements.

These tools require the design and/or paper edges to be identified via ROIs. When running one of these measurement tools, they look in the ROI manager for an appropriately named ROI first. If a single usable ROI is found, then it is used. If multiple appropriate ROIs are found, then the user is ask to select the one to use. If no appropriate ROIs are found, then the user is prompted to create the required ROI(s) – these new ROIs are automatically placed in the ROI manager with an appropriate names.

We have three measurement functions. The first two are quite simple: Measure Design & Measure Paper. They simply measure the design (or paper) and the its bounding box, and place/update a bounding box ROI in the ROI manager. Both the ROI and its bounding box are measured because these two functions do not require the ROIs to be rectangles – so the two measurements might be different.

The most interesting command is the Centering Report option which pops up a dialog box with a number of measured values related to centering & margins. The centering report requires both a paper and a design ROI, and the paper ROI must be a rectangle. A "margin" is a rectangular ROI of maximal size between one edge of the paper ROI and the design. They are denoted in yellow in the image below.

The Create Special Stamp ROI menu option automates the creation of some useful ROIs given a reference point on a stamp. For example, by identifying the upper left corner of the design frame, the system can automatically create a design ROI. Of course the sizes of and locations of such ROIs will differ by issue, and so the system is driven by a user extendable list of rules for how to make ROIs. Here is the configuration file that ships with PhilaJ:

# Stamp ROI Rules
#
# The idea is to define handy rules that can automatically create ROIs (i.e. selections in ImageJ) given a
# reference point.  Usually that reference point is the upper left design frame corner.  This file is a CSV with
# each line describing a single rule.  The first column is the "name" of the rule.  This name is what appears in
# the menus presented by PhilaJ.  The second column is an ROI name.  This will be used to name the ROI after it is
# created -- so you could hit "T" to add it to the ROI Manager and have a nice name.  The remainder of the items on
# the line describe a set of selections that will be joined together (as if they were drawn with the "shift" key
# down.  Each selection is a semicolon separated list of parameters: Selection type (rectangle or polygon), and a
# list of numbers to define the selection.  The numbers are all in millimeters, and are offset by the "reference
# point".  For a rectangle the parameters are x, y, width, and height.  For a polygon, the list is of variable size
# and consists of x & y coordinates for the vertexes.
#
# Lines starting with # are comments
#
Bari Wolf Design (full),design-full,rectangle;0.000;0.000;23.070;27.540
Bari Wolf Design (frame),design-frame,rectangle;0.000;0.000;23.070;26.544
Bari Wolf Color Sample (wolf),color-wolf,polygon;15.740;13.240;17.816;15.465;17.752;14.660;16.037;12.838,polygon;8.686;15.041;8.347;17.710;8.791;17.647;9.130;14.871
Bari Wolf Color Sample (burlage),color-burlage,polygon;17.964;6.186;17.880;7.203;18.769;7.923;18.981;7.648;18.113;7.076;18.155;6.207
BEP AM Post Design,design,rectangle;0.000;0.000;19.511;22.319

The configuration file is called "stampROIRules.csv", and is located in the PhilaJ Configuration Directory. If the file is missing, then the ROI tool will have no rules, and generate an error message.

The Coordinate Tool is used to identify "X,Y" coordinates in millimeters on the surface of an object (stamp, sheet, cover, etc…) with an arbitrary origin reference point. It can be used as a more precise replacement for the Thirkell position finder when the reference point is the upper left corner of the design bounding box. In addition, the Coordinate Tool has more sophisticated options for documenting points and regions via ROIs and saved image files.

The coordinate tool may be started up via the Coordinate Tool or Coordinate Tool Options menu selections. The second provides a chance to change the tool settings before drawing the overlay:

If an ROI is active when the tool is started up, then a popup will ask if the coordinate origin should be set to the upper left hand corner of the current ROI's bounding box. If this ROI has an SID, then it will be stored in the "ROI Name SID" field of the options dialog. Unlike the Position Finder tool, this the coordinate reference point may be freely moved around on the image using the PhilaJ Overlay Interaction Tool (by holding down the [shift] key and dragging with the left mouse button).

Like the Position Finder tool, clicking on the image with the PhilaJ Overlay Interaction Tool active adds a point to the the measurement results with additional columns "relX" & "relY" – the distance right and down from the origin in millimeters. Note a pair of lines are also temporarily drawn on over the image connecting the point clicked to the X & Y axes of the coordinate system – this is only drawn when the option "Draw Point ROI Axis Guides" is selected in the options dialog. Also note the complex name for the ROI in the measurement window – this name is controlled by the following options: "ROI Name Prefix", ROI Name Coords", "ROI Name Box Size", and "ROI Name SID".

One additional feature is the ability to quickly make rectangular selections and even save them to disk. My primary use case for this feature is to document plate flaw locations and make tiny JPEGs for inclusion into my albums. These rectangular selections are made just like the point selections already discussed, but the [control] key is pressed while clicking. Note the image below has no "Axis Guides" because the option "Draw Box ROI Axis Guides" was not selected when this selection was made – the default. Also note that we have two entries in the measurement results window. The first is for the point we clicked on, and the second is for the region. In this case both ROIs have different names, but some combinations of naming options can lead to the two ROIs having the same name. In addition to having measurement window entries, we also have a new ROI in the ROI manager this time – because we had the "Save box ROIs in the ROI Manager" option selected before we clicked. Note some combinations of naming options can lead to the two ROIs having the same name.

The size of the selection is determined by the tool options. The precise location of the selection is influenced by the "Image Coordinates in JPEGs" option. If it is set to "pixels" or "thirkell", then the rectangle will be precisely centered on the point clicked. If it is set to "physical" and the region is bigger than 3mm, then the upper left corner of the selection will be on an even millimeter coordinate point. This "rounding" of the upper left coordinate point allows us to communicate the location of the flaw image in even millimeter values. If the option "Save Box Images" is selected, then a JPEG of the box will be saved (For more information see the section: Making Images From Selections). The image name will, by default, contain the size and coordinates of the selection. Here is the JPEG for the previous selection:

Note the "thirkell" option for units will put the Thirkell coordinates of the point clicked in the JPEG file name. These coordinates are based on the origin of the Coordinate Tool and a 3mm grid size. Note the region may be set larger or smaller if desired, but the coordinates will always be based on the standard 3mm grid size of the Thirkell Position Finder.

Note the "physical" option always means "millimeters" because all images in PhilaJ are scaled in units of millimeters.

The idea is to identify the location of plate flaws (or anything really) using coordinates in terms of the upper left corner of the design. Starting with the upper left corner of the design bounding box we enumerate a grid system (letters on the vertical and numbers on the horizontal). The traditional grids are 3mm as used on the Thirkell position finder. This tool allows one to use different sizes of grids. When invoked it looks for a design ROI. If one is found, then it is used. Otherwise the user is prompted to create one (it will be placed in the ROI manager for the user for future use). Like most PhilaJ overlays things like the fonts and colors may be adjusted. x

This tool is started via the Position Finder or Position Finder Options menu selections with the second option showing an options dialog before drawing the overlay:

Like many PhilaJ overlays, this one may be interacted with via the PhilaJ Overlay Interaction Tool. If the image is clicked on, then the coordinates of the point clicked will be added to the measurement results window. If an ROI is defined, and the Overlay/ROI Measure command is used, via the uppercase [M] key, then the ROI will be measured and an extra column will be added to the results for the position finder coordinates. In the following image, the first measurement result line is for a clicked pint and the second is for the highlighted ROI.

I find this tool most useful when referring to literature that uses the Thirkell position finder. For practical plate flaw locations, I tend to use the Coordinate Tool more useful.

We are frequently concerned with parallel edges like the straight edges of a coil stamp, paper edges of a souvenir sheet, or rows of perforations. PhilaJ provides a generic tool to measure the angle and distance between arbitrary edges in the Angle & Distance Between Edges menu item. This tool will prompt the user to make two line selections, and then report some statistics in a popup:

It also provides a more specialized tool for US coil stamps in the Coil Edge Check menu item. This tool will make use of ROIs stored in the ROI Manager with names like coilEdgeB, coilEdgeL, coilEdgeR, and coilEdgeT. If no ROIs are found, then the user will be prompted to make line selections, and the tool will save off these selections in the ROI Manager with appropriate names. When ROIs are specified, a final report is displayed in a pop up and the edges used are highlighted on the image.

The Grill menu option is used to draw a template of a grill over a stamp image – so one may compare the grill marks on a stamp with a template of the suspected grill type. When the grill tool starts up it looks in the ROI manager for an ROI named "grill" or "grillPts". If one is found, then it is used to place the grill template over the stamp image. If none are found, then the user will be prompted to draw a rectangle around the grill – this newly created grill ROI will be placed in the ROI manager.

I find it easier to identify a handful of grill points on the edges of a grill than to identify the grill boundary sometimes. The intent is that the "grill" ROI be a rectangle outline of the grill, while the "grillPts" ROI is a multi-point ROI identifying grill points.

When invoked via the "Grill" menu selection, the overlay is immediately drawn using the previous, or default settings. By default an "E" grill is drawn with 17 vertical points. This may be changed by using the Grill Type & Options menu selection to start the tool. This selection will first show a grill type selection dialog:

This dialog will be followed by the grill options dialog, the same dialog you get when you use the Grill Options menu selection:

It is typical to toggle through a grill or two in order to find the one that fits best. Note the options dialog contains the usual customization options like line color and width, but it also contains several options regarding what parts of the grill template are drawn. For difficult grills it is worth playing around with these options.

The PhilaJ Overlay Interaction Tool allows one to drag the grill template around on the screen, but you must update the "grill" or "grillPts" ROI to make the grill appear in the new location for future invocations of the grill tool. This may be easily done via the Overlay/ROI Measure command, bound to uppercase [M] – this will create/update an ROI named "grill" in the ROI manager with the current grill outline. This is also a handy way to convert a "grillPts" ROI into a rectangular "grill" ROI.

The Separate stamp multiple menu option breaks up images of stamp blocks into stacks of individual images. When activated the following dialog will appear:

The first two requested numbers define the block size, and are used later by PhilaJ to separate the sheet into stamps. The second two values are used to label the stamp images with the position number from the original sheet from which the block came:

• The sheet position of the upper left stamp – if you don't know, then set it to "-1".
• The width of the sheet from which the block came – if you don't know, then leave it as is.

In the example here, we have a 7x2 block taken from the lower left corner of a 10x10 sheet. Thus the upper left stamp in our block was position 81 in the original sheet. If you don't know what values to use for sheet position, set the first to "-1" – this will number the stamps consecutively starting at 1. Using "-1" also causes a subtle change in the resulting slice names in that they will be simple numbers instead of being prefixed by "p" – this is related to recommended SID values documented in the section About ROI Name Components. The remaining options are used to specify how the image overlay will look – in this case we have selected pretty wide lines (so I can include nice screenshots), red division lines & text, and green for the "block ROI" discussed next).

After the dialog, the tool will ask the user to define a "block ROI". This ROI should define the outer edge of where we would cut the stamps (see image below).

The tool will then split the block into stamp sized rectangles with boundaries between stamps. Sometimes these boundaries miss because the original ROI was improperly positioned. For this reason, the tool will ask the user if the cut lines are acceptable. If they are not, then the user is requested to adjust the block ROI. This process repeats until the user accepts the cut lines. Then the tool will extract an image for each stamp, and place them all in a single ImageJ image stack. Here is what a good set of cut lines look like:

Note that this final block ROI will be saved in the ROI manager with the name "multipleOuterSep".

One of the best ways to spot plate flaws is to "align" these stamp images, and then flip through the images in the stack allowing the natural ability of the human eye to notice changes. How do we align the images in the stack? I find it useful to first crop the images so that we just have the designs – no perforations. Do that by making a rectangular ROI, and then use the "Image -> crop" menu option. In the image processing field, the problem of aligning images is called "image registration". Because this is a very common problem in many fields, ImageJ has several plugins available for the task. For stamps, I have found "plugins -> Registration -> linear stack alignment with SIFT" to work very well.

The Make Design ROIs for Multiple menu option is designed to partly automate the creation of design ROIs for multiples. The resulting ROIs usually need to be individually adjusted, but this is much less work than creating each ROI from scratch. In practice it works much like the Separate stamp multiple tool. When The Make Design ROIs for Multiple menu option is selected, the user is presented with a dialog box:

For the most part, this dialog like the Separate stamp multiple tool. The use of "-1" for the sheet position will cause the resulting ROI names to be "design_# instead of "design_p#" – i.e. the SID won't be prefixed by a "p". This is related to recommended SID values documented in the section About ROI Name Components.

After the dialog box, the tool will ask the user to identify the upper left stamp design like so:

Next the tool will ask the user to identify the lower right stamp design like so:

The generated design ROIs will then be displayed, and the user will be ask if the ROIs should be saved in the ROI manager:

If the user instructs PhilaJ to save the ROIs, then ROIs will be created and saved in the ROI manager:

The Rotate Line to Horizontal menu option rotates an image so that the current line ROI will be horizontal. That is to say, draw a line on something that should be horizontal in the image (frame line, row of perforations, paper edge, etc..), and use this function to rotate the image. This menu function is also bound to the [1] key.

The Rotate 90 Degrees Right menu option's function is pretty much obvious. It is also bound to the [2] key.

Both of these rotation commands will clear the current overlay. To redraw it, hit the [g] key.

Note that image rotation can make future linear measurements impossible. Please read the section Capturing and adjusting properly scaled images.

ImageJ is perfectly capable of creating new images from a selection with "duplicate" command (bound to the "d" key). When run with an existing ROI, the "duplicate" command essentially performs three steps: 1) "Edit -> Selection -> To Bounding Box", 2) "Edit -> Copy", 3) "File -> New -> Internal Clipboard". PhilaJ provides two ways to do something similar.

The first is Selection to image (with scale) which creates a new image from the current ROI's bounding box, and then copies the source image scale to the new image (if the source had one). The second is Selection to JPEG, also bound to the uppercase [J] key. This one is a bit more specialized. It is intended to immediately save a JPEG of the new image to disk leaving no new image open in ImageJ.

Both Selection to image (with scale) and Selection to JPEG use the same underlying system to create a name for the new image. The name may contain several components:

• The base name for the source image
• Coordinates of the bounding box (upper left-hand corner) in pixels, physical units (millimeters), or Thirkell notation.
• Size (width, height, or both) of the bounding box in pixels or physical units.
• SID for the ROI.
• Name of the ROI.

What gets included is controlled by the dialog:

Note the options available in the "Additional Image Name Annotation" section will dynamically vary depending on the situation. For example if the image has no scale, then the options for "Pixel Coordinates" & "Thirkell" won't be available. In a similar way the options "ROI Name" & "ROI SID" will not be shown if the ROI has no name. Also note the defaults for some options can be set by the calling method. For example, when called from the Coordinate Tool the default value for the "Include width & height in coordinates?" option will be unchecked. As another example, the primary difference between the Selection to image (with scale) and Selection to JPEG is the default value for the "Automatic Save Actions" option.

Note both Selection to image (with scale) and Selection to JPEG behave differently if called while the Position Finder or Coordinate Tool overlays are active. In this case the coordinates are relative to the origin of the coordinate system.

The Create Preview & Thumbnail Images menu option creates smaller copies of an image for use in web pages. This is the saem operation preformed by the Process a directory of scans menu otpoin, but broken out for ad-hoc use.

The menu item Overlay/ROI Measure, also bound to the uppercase [M] key, is intended to largely replace and extend the behavior of the built in "Measure" function bound to the lowercase [m] key.

Overlay/ROI Measure preforms a sequence of actions. First it saves the measured ROI in the ROI Manager with a name of "philMeasured" – if an ROI already exists with that name, then it will be removed first. Next it calls the built in "Measure" function – note the name of the ROI when measured will be the name the ROI had when Overlay/ROI Measure was called – not "philMeasured". Lastly Overlay/ROI Measure will preform an overlay specific action for the following overlays:

• Dynamic Perforation Gauge
• Position Finder
• Grill

ROI offsets are closely related to centering, but are more about things that should be in a particular place but are not. For example, if a press comes down on a sheet twice in a perfect world, it would hit the same place. But when they don't we can see two impressions with one offset from the other. As an example, consider the following image. The popup in the middle is what you get when you use the Offset Between ROIs tool, and select the two deign frames.

Note the offsets are measured in terms of the distance between the upper left of each ROI's bounding box.

The PhilaJ Load image & ROI sidecar. Attempt to set Scale. menu option, also bound to lowercase [o], cause a sequence of actions: first an image is loaded, then ROIs are loaded via Load ROIs from PhilaJ sidecar file, and then PhilaJ attempts to set the image scale using the following sequence of steps (stopping when one of them works):

• If ImageJ set the scale automatically, then PhilaJ will attempt to covert the scale to millimeters via Convert image scale units to mm. This most commonly occurs when ImageJ uses an embedded TIFF DPI tag created automatically by a document scanner.
• Next it attempts to use Set scale from DPI file name
• Next it attempts to use Set scale from scale ROI
• Lastly it will attempt to use Set Scale for Stereo Microscope Photograph if the image is located in the RPI image directory (normally "$HOME/Pictures/pi-cam").

The PhilaJ Save image & ROI sidecar menu option, also bound to lowercase [s], saves the file, and an ROI sidecar file if the ROI manager is non-empty. Note that PhilaJ always saves a file as a PNG or TIFF file – a PNG if the file is a simple image with one slice and a TIFF otherwise.

The SaveAs image & ROI sidecar, bound to uppercase [S], is similar except it allows the user the change the filename first.

PhilaJ associates a "sidecar" file containing ROIs with each image file. Essentially PhilaJ expects to find ROIs associated with an image file saved off in another file of the same name and an extension of ".roi.zip". For example, if your image file was named "foo.png", then the sidecar would be named "foo.roi.zip".

We can save and load sidecar files for the currently active image with the menu options Load ROIs from PhilaJ sidecar file & Save ROIs to PhilaJ ROI sidecar file..

Similar to ROI Sidecars, PhilaJ can load a text file associated with an image via the Load Notes from PhilaJ sidecar file menu entry.

Note sidecars are not as integrated into PhilaJ as are ROI Sidecars. These files are not automatically loaded by Load image & ROI sidecar. Attempt to set Scale.. They are also not automatically saved by Save image & ROI sidecar or SaveAs image & ROI sidecar. Finally, they are not automatically renamed when the image is renamed.

The Convert image scale units to mm menu option attempts to convert the current image scale units to millimeters for PhilaJ. For example, if an image scale was specified in DPI via an embedded TIFF tag, this will convert it to millimeters. It only knows about the most commonly used length units in philately:

• mils – thousandths of an inch
• inches
• centimeters
• meters
• micrometers

PhilaJ has two tools that can resize an image with the end goal of changing the image scale. In both cases, an image with different horizontal & vertical scales will be resized so that the pixels are as square as possible. The difference is in how the resize is preformed.

The first menu option is Shrink image to make pixels square. This command only shrinks the image, and then only horizontally or vertically – not both. The second option is Resize image to target DPI. This one resizes the image to hit a target DPI. In doing so it might shrink or grow the image, and it might resize both horizontally & vertically. The first option minimizes both distortion and data loss. It is the best choice for precision measurement. The second option is more useful when resizing an image so that it may be printed/published at a desired size.

It is important to make pixels square before an image is rotated. Failure to do so will make future linear measurements impossible. Please read the section Capturing and adjusting properly scaled images.

PhilaJ contains two commands that work directly with a special ROI to set or save image scale:

• Set scale from scale ROI
• Create scale ROI and add it to the ROI manager

While these can be called via the scale menu, the first is automatically called when using the PhilaJ file open command (The [o] key).

Scale ROIs have a special format for the name: "scale_<NUMBER>mm"

If the scale ROI is a line, then "NUMBER" is its length in millimeters. If it is a rectangle ROI, then "NUMBER" is its width in millimeters.

When the scale ROI is a line, then image pixels are assumed to be square. When it is a rectangle, the height of the rectangle is used to set the pixel aspect ratio.

PhilaJ can create a rectangular ROI for a scaled image and place that ROI in the ROI manager. PhilaJ will always create rectangular scale ROIs even when the pixel aspect ratio is 1.

The built in ImageJ set scale dialog may be accessed via the PhilaJ scale menu using the option Set Scale via standard ImageJ dialog. In addition, this menu provides four other interfaces to the same command that might be more directly useful for stamp images.

• Set Scale 1D
  This menu option provides a simple way to enter known distances in pixels and millimeters, and sets the scale. The distance in pixels can be prepopulated from the distance of a line ROI if one is active when the menu is selected. This is much like the built in scale command, but forces the use of millimeters.
• Set Scale 1D from measurement results table
  This menu option works just like the previous except it takes the distance in pixels from the last measured value in the measurement results table.
• Set Scale 2D
  This menu option provides a more direct way to set the scale for an image with different horizontal & vertical scales. Instead of asking for a scale ratio like the built in command, it requests known distances in pixels & millimeters in both the horizontal and vertical direction. This is usually a simpler for philatelic work because we are using 1) a scanner with known horizontal & vertical DPI, or 2) we are using a right angle measurement scale in the photographic field.
• Set Scale 2D from measurement results table
  This menu option works just like the previous, but it takes both the horizontal (measurement #1) & vertical (measurement #2) distance distance in pixels from the last two measurements in the measurement results table. When using a right angle measurement scale, the typical procedure is to draw the vertical scale ROI, hit [m], draw the horizontal scale ROI, hit [m], and then invoke this function.

Note the default distance in millimeters for all of these options is \(50\,\mathrm{mm}\) because I use \(50\,\mathrm{mm}\) glass scales graduated to \(\frac{1}{10}\,\mathrm{mm}\) for both my scanner and microscope.

The Set scale for DPI allows the user to set the image scale directly via a DPI value. This value is converted into millimeters automatically. Modern scanners frequently have different DPIs horizontally & vertically, and that is where the Set Scale for Hoiz & Vert DPI menu option comes in.

Lastly, several common DPIs may be set via a handful of options at the top of the scale menu:

• Set scale for DPI: 2410x2398 – This odd DPI is what I get at the center of the platen on my Epson scanner. ;)
• Set scale for DPI: 2400
• Set scale for DPI: 1200
• Set scale for DPI: 600
• Set scale for DPI: 300

The Set scale from DPI file name menu option extracts DPI information encoded in the filename of the current image. This is probably best explained via examples:

• "foo_2400dpi.jpg" – Set the DPI to 2400
• "foo_2400.123dpi.jpg" – Set the DPI to 2400.123 (that is to say, the DPI need not be a whole number)
• "foo_2300vdpi_2500hdpi.jpg" – Set the vertical DPI to 2300 and the horizontal DPI to 2500.

When loaded via the PhilaJ Load image & ROI sidecar. Attempt to set Scale. command, a DPI encoded in a filename like this will automatically be used to set the image scale. Thus this command is most useful when an image has been loaded in another way – like via the "file -> open" command in the main ImageJ menu.

Some of the data PhilaJ houses for doing computations can come in handy for the humans using the tool.

The Kiusalas Table menu item will display a table of US Kiusalas values, the value reported in the Scott Catalog, and the standard perforation measurement to four digits.

The Grill Table menu item will display a table of US grill characteristics.

The Measure Color menu option is used to produce a report regarding the colors of the currently selected pixels. The traditional Red/Blue/Green scheme of describing digital colors is not used by PhilaJ. Instead the CIELAB color space is used for all PhilaJ color computations and reporting. With CIELAB colors are described via three quantities: \(L\), \(A\), & \(B\). In addition, two useful quantities may be computed from these: \(C\) & \(H\). The most important quantity is \(H\), known as the Hue Angle, as it is a good, single number representing the "shade" of a color. This is an angle measured in degrees and always in the range \(0\) to \(360\). I have been pretty successful using this number to identify some difficult stamp shade varieties. PhilaJ also reports another angle, \(J\), which I call "Jue" – in Spanish the "J" is frequently pronounced as an "H". \(J\) is simply \(H\) centered at zero and ranging from \(-180\) to \(180\) – logically it is equal to \(H\); however, it is useful when measuring colors with a hue angle distribution that covers a range around zero.

When activated, Measure Color menu option can produce reports in two windows:

• A statistical summary of the colors (max, min, mean, and standard deviation for all five variables: \(L\), \(A\), \(B\), \(C\) & \(H\))
• A histogram of the one of the channels. By default the option is "H or J" which will pick the channel with the lowest standard deviation – this is an attempt to pick the "best" option between \(H\) or \(J\) that will deliver a nice Histogram.

The report windows will include the name of the ROI measured!

If the menu option is used on another selection or with another image, then new histogram and statistics windows will be created allowing the user to compare colors. Note the Compare Two Colors menu option provides some automation and additional computation for comparing colors.

PhilaJ can convert a few units philatelists frequently encounter. Perforations may be converted between "hole gap in thousandths of an inch" (i.e. Kiusalas) and "holes per 2cm" (i.e. what is in most catalogs) via:

• Convert Kiusalas to Perforations per 2cm
• Convert Perforations per 2cm to Kiusalas

These functions pop up a dialog box asking the user to enter the value to convert, and then pop up a window with the answer.

Much of PhilaJ's functionality is centered around linear distances measured in millimeters; however, sometimes we get values in other units. The Convert length to millimeters menu item allows one to convert various other units to millimeters.

Lastly the Convert Distance to Perforation Measurement menu item "converts" distance into "holes per 2cm". This isn't really a straight up unit conversion like the other commands documented in this section; however, I include it in the menu because some older catalogs measure perforations as a count over a distance other than 2cm. The idea is that you have \(N\) perforation holes, and measure the distance from center to center (or edge to edge) for the holes, then you can compute the perforation value in standard units. Like the previous functions, this one will pop up a dialog box asking for distance and hole count. If you have an active line ROI when the menu is selected, then the length of the line will be used to prepopulate the distance value. If that line ROI happens to be one that was previously created by the Dynamic Perforation Gauge, then the number of holes will also be prepopulated. The results window provides standard perforation and Kiusalas units.

The Scale Report menu option produces a short report in a popup regarding the current image scale. This is a handy report because it bridges the gap between the various ways image scales are usually reported. Many times a US philatelist will be working in DPI while a colleague in the EU may be working in PPMM. Another common scenario is having some images captured via a digital video camera or microscope camera where scale is frequently expressed as pixel size in \(\mu\mathrm{m}\) and other images of the same specimen from a document scanner calibrated in DPI.

Philatelists frequently have a great many scans or captures to deal with. Be it a marathon album scanning session or a detailed analysis of a single, valuable specimen.

PhilaJ provides a semi-automated method to scale for square pixels, rotate, crop, save, and create a thumbnail file. I say semi-automated in that as PhilaJ processes each image the end user is required to draw a line for a rotation to horizontal and draw a rectangle for the final crop. This routine is accessed via the Process a directory of scans menu option.

Note: Other software can do this stuff in a fully, or almost fully, automated way. The only issue with these fully automated solutions is that most of them do not make image size adjustments to square the pixels before they rotate the images into alignment (See the section Capturing and adjusting properly scaled images for more). That said, if you are just doing a bulk album scan, then these tools are well worth the time to acquire and learn how to use.

The Stamp Crop w/ Previous Settings & Stamp Crop w/ New Settings menu items assist in making more uniform, and repeatable image crops. The system is driven by a user extensible set of "crop rules" that define the way an image is cropped under user control. Most of this is best described in the comments in the configuration file:

# Crop Rules
#
# This is a CSV file (Comma Separated Value) used to describe PhilaJ "crop rules".  Crop rules define a method for cropping
# an image in PhilaJ.  In this file each line defines a rule.  The first column of each line is a "name" for the crop rule.
# This name will appear in the menus presented by PhilaJ.  The next item is the type of crop rule.  At the moment only two
# types exist:
#
#         1) margins
#         1) margins+box
#
# The "margins" type rules are followed by four numbers: Left Margin, Top Margin, Right Margin, & Bottom Margin.  These
# values are in millimeters!  This kind of rule prompts the user to make a selection, then pads the selection's bounding
# box with the specified margins, and crops the image.  This is a handy way to crop stamp images -- draw a rectangle about
# on the edges, and then let PhilaJ add 1mm padding to the crop.  That way we get nice, uniform margins on our scans and
# it's less fiddly to get them right.
#
# The "margins+box" type rules are followed by six numbers.  The first four are the same as with "margin" type rules: Left
# Margin, Top Margin, Right Margin, & Bottom Margin.  The remaining two are: Box Width and Box Height. These values are in
# millimeters!  This kind of rule prompts the user to identify the location for the upper left corner of the "box", then it
# crops the image using the box and margins.  For example this allows the user to crop a stamp to the design while only
# needing to click on one point -- the design's top left corner.
#
# Lines starting with a # are comments.
#
Rectangle + 5mm margins,margins,5.000,5.000,5.000,5.000
Bari Wolf Design + 1mm,margins+box,1.000,1.000,1.000,1.000,23.409,27.466
AMG BEP Design + 1mm,margins+box,1.000,1.000,1.000,1.000,19.511,22.319

The configuration file is called "stampCropRules.csv", and is located in the PhilaJ Configuration Directory. If the file is missing, then the crop tool will only have the "rectangle" and "Rectangle + 1mm margins" rules available.

The Create ROI Annotated Image menu item will create an image with each ROI drawn – right now plate flaw and fault ROIs are supported. This is accomplished by searching the ROI Manager for ROIs with names staring with "pflaw", adding them to the overlay, and then flattening the image. Some effort is made to intelligently place the string "_pflaws" in the new image title to make saving the image less annoying. Note that plate flaw ROIs may be created manually or with the assistance of the Coordinate Tool. Note that if you intend use Create Preview & Thumbnail Images on the resulting image, it is best to set the line width high enough that the ROIs are still visible when shrunk down to thumbnail size.

PhilaJ can pop up quite a few windows, and when loading a new image most of those windows won't be helpful. Closing all those windows by clicking on the close buttons is a pain, so PhilaJ provides a few helpful menu items:

• Close PhilaJ Windows
• Close PhilaJ & Related Windows
• Close Image, PhilaJ, & Related Windows

Frequently we don't just want to close the windows, we want to also delete the image file at the same time. This is very common with microscope images that we snapped for a quick analysis. In these cases, the following menu options may be useful:

• Delete current image file
• Delete current image file & close image window
• Delete current image file & close associated windows

The Bulk ROI Rename menu option is a powerful way to rename ROIs; however, it can can be quite dangerous. I strongly suggest saving the ROI Manager contents first. This tool asks the user for a search and replacement string. It then replaces every occurrence in the names of the ROIs in the ROI Manager.

The menu option Clean up ROI list preforms several actions:

• Rename old style ROI names. Older versions of PhilaJ used different standard ROI names. This tool transforms the old style names into the new style names.
• Delete any ROIs with a duplicate name – leaving just one ROI with any given name.
• Delete any margin ROI with no associated design & paper ROIs.
• Delete any BB ROI without a corresponding ROI for which it could be the bounding box
• Delete "pfHole" ROIs without matching "pfLine" ROIs
• Regenerate the "ALL" ROI
• Pop up a window with a report of all the changes.

I suggest saving the ROI Manager contents first. That way you can undo the cleanup.

• Items in square brackets are not required, but items in angle brackets are required.
  • Example 1: pfLine<NN>_<SFX>
    • GOOD: pfLine12_foo
    • BAD: pfLine_foo, pfLine12, & pfLine
  • Example 2: design[_<SID>][-<SFX>]
    • GOOD: design_foo-bar, design_foo, design-bar, design
    • BAD: design_ – i.e. if you have the "_" you must have the "SID" too!
• Items separated by hashes are mutually exclusive options
  • Example: coilEdge<B/L/R/T>
    • GOOD: coilEdgeB, coilEdgeL, coilEdgeR, coilEdgeT
    • BAD: coilEdge & coilEdgeBL

• <B/L/R/T> - Used to indicate side (Bottom, Left, Right, Top)
• <NN> & <MM> - zero padded integers – i.e. "01" but not "1"
• <SID> - Used to identify the stamp an ROI is associated with.
  • Rules:
    • Should be alphanumeric (letters and numbers)
    • Must not contain a dash ("-")
  • Recommendations
    • Sheets & if you know the sheet position: Use pN – the "p" is for position, and "N" is the number.
    • Blocks: Integers starting with 1 at the upper left and going left to right & top to bottom.
    • For large multiples, zero pad the integer so the SID integers are all the same width and thus sort correctly
    • For pairs use L (Left) & R (Right) or T (Top) & B (Bottom)
• <SFX> - Used to differentiate an ROI from others with the same name
  • Rules:
    • Should be alphanumeric (letters and numbers)
  • Examples
    • "design_1-center" & "design_1-frame" might be use for a classic, bi-color US stamp
    • "design_1-A" & "design_1-B" might be use for a stamp with a double impression

• For perforation ROIs (pfHole<NN><MM>_<SFX> & pfLine<NN>_<SFX>)
  • For single stamps I normally use: T (Top), B (Bottom), L (Left), & R (Right) for the PFX
  • For vertical coils: T (Top), B (Bottom), C (C center)
  • For horizontal coils: L (Left), R (Right), C (C center)
  • For horizontal strips: T (Top), B (Bottom), R1 (Row 1), etc…
  • For vertical strips: L (Left), R (Right), R1 (Column 1), etc…
  • For blocks/sheets: R1 (Row 1), C1 (Column 1), etc…
• pt_<TAG>_<N>
  • For grill points set the TAG to grill.
  • For design coordinates use d or design. For multiples use design_<SID> – i.e. the design ROI for each stamp.
  • For imperf souvenir sheets use edges

• In image processing, a "bounding box" is the smallest rectangle with sides parallel to the image edges that contains some object
• Most ROIs can be associated with a bounding box ROI with a "BB" in the name.
• Most "BB" ROIs are created by automatic computations (centering or grill measurements for example)
• Examples:
  • "designBB_top-frame" is a bounding box associated with the design ROI "design_top-frame"
  • "overlayBB_1" is a bounding box associated with the design ROI "overlay_1"
• HR ROIs are "Horizontal Reference" lines
  • In image processing, a "horizontal reference" is a line that indicates the natural horizontal of an artifact
  • These are not necessarily associated with another ROI, but they can be
  • Most HR ROIs are manually created by the end user instead of by automatic computations
  • Examples:
    • An text overprint might not be quite level. If the overprint is identified by an ROI named "overprint_UL-red", then the horizontal reference ROI would be named "overprintHR_UL-red".
    • Note that an associated ROI need not exist – i.e. the "overprint_UL-red" ROI in the previous example isn't strictly necessary.

• Some macros will look in the ROI manager for specific ROI names or name patterns, and use them if they are found.
  • design[_<SID>][-<SFX>] - Design & centering measurements
  • paper[_<SID>] - Paper & centering measurements
  • grill[_<SID>][-<SFX>] - Used to draw grill templates & to measure a grill
  • grillPts[_<SID>][-<SFX>] - Used to draw grill templates & to measure a grill
  • scale_<X>mm - used to set image scale
• In addition, some ROIs will be created and added to the ROI manager if they are needed and don't already exist.
  • design - Design & centering measurements
  • paper - Paper & centering measurements
  • grill - Used to draw grill templates & to measure a grill
  • coilEdge<B/L/R/T> - Coil edge angle measurements
• Some macros will construct ROIs and save them in the ROI manager for the user.
  • designBB[_<SID>][-<SFX>] - Design bounding box created by a design measurement or centering report
  • paperBB[_<SID>] - Paper bounding box created by a paper measurement or centering report
  • margin<B/L/R/T>[_<SID>][-<SFX>] - Rectangular selection for the margins (gap between a design & a paper) created by the centering report
  • grill[_<SID>][-<SFX>] - Constructed from a grillPts ROI
  • scale_<X>mm - Created by the scale ROI maker
  • pfLine<NN>_<SFX> - The span of a perforated edge created by the dynamic perforation gauge
  • pfHol[<NN><MM>_<SFX> - Marks a perforation hole created by the dynamic perforation gauge
  • philMeasured - Last ROI measured by my the PhilaJ ROI measure function (M key)
• Some macros will construct ROIs, but not place them in the ROI manager
  • dynPf_<NN>_perfs - Constructed by the dynamic perforation gauge when not using the ROI manager
  • mmcPt - Constructed by the coordinate tool for measured points
  • mmcBx - Constructed by the coordinate tool for measured rectangles
  • mmcBxGuide - Constructed by the coordinate tool – drawn guides for boxes
  • mmcPtGuide - Constructed by the coordinate tool – drawn guides for points
• Some macros will use the current selection name & update the ROI manager with the current selection:
  • design[_<SID>][-<SFX>] - Design & centering measurements – centeringReport() & measureDesign()
  • paper[_<SID>] - Paper & centering measurements – centeringReport() & measurePaper()
  • grill[_<SID>][-<SFX>] - Used to draw grill templates & to measure a grill
  • grillPts[_<SID>][-<SFX>] - Used to draw grill templates
• Some macros will use the current selection name & extract extra data for computations
  • <PFX>_<NN>_perfs - Used by computePerfsFromDistance() & drawDynPfOnLine()
• Some ROIs are not currently used by any macro
  • pf_<SFX>
  • fault_<SFX>
  • wmark_<SFX>
  • pn_<N>
  • idFact_<SFX>
  • pmark_<SFX>
  • overprint[BB/HL]_<SID/SFX>

Capture, save, and open an image from the camera. Images are stored in the same location, and with the same file name conventions, used by piSnap.sh.

Change some configuration options

• Specify a group for the captured image filenames.
• Specify an annotation for the captured image filenames.
• Set captured image format (jpg or png)
• Set captured image scale (100% or 50%)
• Set the scale factor for capture preview
• Set the scale factor for the live video feed
• Turn on/off asking for settings for each capture – essentially pops up the settings dialog box everything the capture button is hit
• Turn on/off repeated capture mode – repeatedly captures images. Most useful if a group is set.
• Turn on/off live video preview before a capture.
• Turn on/off loading images after capture.
• Turn on/off running the set image scale tool after each capture if the image scale is not already set
• Turn on/off debugging

Live video feed from camera. Note the scale setting for the live video feed is different from the capture preview scale.

If "Change Settings Before Capture" is set, then a simplified settings dialog box will appear before the video feed window.

Load previous capture(s) from camera using the ImageJ/Fiji macro above or the piSnap.sh script.

Set image scale based upon microscope settings. This script contains hardwired settings for my specific microscope and lenses, and may require modification for your microscope.

• The choice of microscope enables a calibration correction factor in the final computation
• The "Adjust for Resolution" option adjusts the scale if the number of horizontal pixels in the image differs from the horizontal resolution of the sensor. Most commonly this use used when the sensor is used in 2x2 mode yielding smaller image. This option also works if the image is resized after the fact.