FossilJ is a plugin for fossil data acquisition by image analysis, using ImageJ.

The plugin provides free, open source tools for semi-automated measurements of fossils, with this first version optimised for bivalve shells with or without predatory drillholes.

FossilJ v0.2.1 was built in the FIJI distribution of ImageJ v1.52n.
FIJI is available to download and explore here: https://fiji.sc/

ImageJ is an open source Java image processing program designed by the National Institute for Health (NIH).
FIJI is Just ImageJ, which comes with many scientific image analysis plugins included and is built on ImageJ2.
For more information about ImageJ, including the macro language, visit https://imagej.nih.gov/ij/index.html and https://imagej.net/ImageJ

Cite as: Fiona Pye, & Nussaibah Raja-Schoob. (2019, July 15). FossilJ (Version v0.2.1). Zenodo. http://doi.org/10.5281/zenodo.3336200
Alongside the ImageJ software you used (see https://imagej.net/Citing).

FossilJ is licensed under a AGPLv3 License.

The documentation for the plugin is available below:

FossilJ Summary:

• FossilJ semi automatically collects morphometric data from images of bivalves.
• The measurements are collected in mm and are:
• width (anterio-posterior)
• height (dorso-ventral)
• broken/complete specimen
• number of drillholes per specimen
• drillhole diameter
• incomplete/complete drillhole
• internal or edge drilling
• Collected measurements are shown in verification images, which can be cross referenced with the data. This data is produced as two CSV files, general specimen data and drillhole data.
• All specimens and drillholes are given numbers which are unique when used in combination with the image name.

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Inputs:

• Input directory containing images with:
• A high contrast between object and background (pale object, dark background).
• Blue scale bar (rgb (0,0,255)) with units of mm or µm (all converted to mm).
• Space between specimens and the edge of the image at ~⅓ of specimen size
• Bivalve shells approximately umbo upwards in the image for chirality determination
• Output directory (empty)

Outputs:

• CSV data
• "shell_measurements.csv"
• Label - Image name
• Width - Anterio-posterior
• Height - Dorso-vental
• Shell - Specimen number (unique per image)
• Broken - Broken shell = 1, complete shell = 0
• Valve - chirality left/right
• "drill_measurements.csv"
• Label - Image name
• Name - Drillhole reference
• Shell - Specimen number (unique per image, same as in "shellmeasurements.csv")
• Type - Internal or edge drill
• Feret - Drillhole diameter
• Incomplete - Incomplete drill = 1, complete drill = 0


• Verification Images ("*" indicates where image name is appended)
Images contain scalebars and specimen numbers
• *measurements - displays length and width measurements
• *valve - shows allocated chirality
• *original_edited - copy of original image with a cleaned black background
• *drillholes - specimens with printed drillhole masks
• *drillholes_drawn - original image with the drillholes as drawn by user

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Setup:
We are currently having issues installing FossilJ as a Plugin, so for now please install it as a Macro (see below).

1. Install FIJI distribution of ImageJ https://fiji.sc/
2. Download the "FossilJ.ijm" file and the "Macros" folder
3. Place the "FossilJ.ijm" file in the "~Fiji.app\plugins" folder
4. Place the files from the "Macros" folder in the "~Fiji.app\plugins\Macros" folder
5. Open ImageJ using the executable file
6. Install the plugin: Plugins tab ⇒ Macros ⇒ Install ⇒ select the "FossilJ.ijm" file
7. Restart ImageJ to finish installation

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Operation:

General Guidance

• User interaction has higher accuracy on larger screens.
• Image windows can be maximised for interaction.
• If contrast between object and background is not suffient, the object may not be detected and will create artefacts in data
• Process up to 15 images together, but no more as if an error occurs the data could be comprimised and may need to be redone.
• Clear, machine-readable image naming system is optimal (for further data analysis).
• Checks on inputs and user verification ensures data quality.
• Clicking "Cancel" at any stage will end this section of the Plugin, but will not exit completely.
  This may cause erratic behaviour. If this occurs click "Cancel" on the next option that appears and close all windows.

Repeat the following sequence on every input folder, until all data is processed:

1. Open FIJI
2. Open FossilJ
   Plugins ⇒ Macros ⇒ FossilJ
3. Select the input and output folders
4. Scalebar calibration
Length and units
Click once on each end of the scalebar then click "OK"
If the scalebar is correctly selected click "Yes" to continue
Verification - to restart calibration click "No". This returns to the length and units input step.
5. Broken Specimens
Type the number of broken specimens into the box and click "OK"
If no broken specimens are present, leave as 0 and click "OK" to move onto the next step
If broken specimens are present, click on each broken specimen once, then click "OK"
Verification - selecting "No" returns to the broken specimen number box, resetting this step.

6. Drillholes
If no drillholes are present leave the default 0 for both options and click "OK" to move onto the next step.
If drillholes are present, put the total number in the top box (complete and incomplete), and the number of incomplete in the lower box and click "OK"
Verification - selecting "No" returns to the drillhole number box, resetting this step.
Follow the instructions provided and only interact with the image when prompted.
The order drillholes are drawn is not important.
Draw the drillhole outer diameter then click "OK". Repeat until all drillholes are outlined, complete and incomplete.
If incomplete drillholes are present, for each incomplete drillhole select the area within the outline once, and click "OK".
Check the identification of the drillhole as edge or internal drilling, which can be edited using the dropdown provided.
7. New Scalebars
When prompted, click "OK" to add scalebars to verification images.
Scalebars appear to the right of the click position, and are 1 mm in length.
Repeat for all prompted images.
8. Valve Chirality
Check the chirality identification (left/right) and edit using the dropdown provided if required.
9. Save
The data and images are saved and closed automatically.