Server connection and monitoring files for CoralCache virtual coral core repository

CoralCT User Guide Video tutorials also available at https://www.sclerochronologylab.com/tutorials.html 1 TABLE OF CONTENTS Downloading .................................................................................................................. 3 Instructions for Mac ............................................................................................... 3 Instructions for Windows ....................................................................................... 4 Opening Program ........................................................................................................... 7 Creating a Working Directory ................................................................................ 7 Creating an Account ............................................................................................. 7 Features of Home Screen ..................................................................................... 8 Selecting a Core ............................................................................................................. 9 Main Menu Features ............................................................................................. 9 Drop-down Menus ............................................................................................... 10 Working on a Core ....................................................................................................... 12 Features .............................................................................................................. 12 Methods .............................................................................................................. 16 Harder Core Help ................................................................................................ 26 CT Density Calibration Curve ..................................................................................... 28 Processing a Core ....................................................................................................... 29 Confidence Interval ............................................................................................. 29 Comment Box ..................................................................................................... 29 Determining Age ................................................................................................. 30 Final Processing Steps ....................................................................................... 31 Submit Data .................................................................................................................. 32 Uploading Scans ................................................................................................. 32 Uploading Metadata ............................................................................................ 32 Uploading Standards .......................................................................................... 33 Modify Data ......................................................................................................... 33 Direct Submission ............................................................................................... 36 Editing Metadata ................................................................................................. 40 Access Data ................................................................................................................. 40 Downloading Data ............................................................................................... 40 Updating CoralCT ........................................................................................................ 44 Mac ..................................................................................................................... 44 Windows .............................................................................................................. 45 2 Downloading Instructions for Mac ● Go to the official CoralCT website (http://www.coralct.org/). ● Scroll down until you see the Mac and Windows options. ● Download MATLAB Runtime 2023a by clicking the bolded “download” link. ● Allow the program to make changes to your computer. ● Choose a destination for this program in your applications. ● Once downloaded, go back to the CoralCT website. ● Download the CoralCT program by clicking the bolded “download CoralCT” link and drag the download into the applications folder. ● If prompted, allow the program to make changes to your computer. ● Once you download CoralCT and try to open the application, you may encounter the following message: 3 ● This is because CoralCT is not registered with Apple. You’ll need to override this. ● Begin by going to the settings on your computer. Find “Privacy and Security” on the left side, then open and scroll down until you see the following. ● Click “Open Anyway” and you will be able to open CoralCT. ● Once in the app, you will be asked to pick the destination. Choose the same. destination as MATLAB Runtime. ● Allow the program to install. This may take a few minutes. Instructions for Windows ● Go to the official CoralCT website (http://www.coralct.org/). ● Scroll down until you see the Mac and Windows options. 4 ● Download the CoralCT program by clicking the bolded “Download CoralCT” link in the Windows section. ● Navigate to your downloads folder and open the installer titled “coralct_installer.exe." ● Once the program is marked as done, click on the box with a diagonal arrow to open the program. ● A blue Microsoft window may pop up saying, “Microsoft Defender SmartScreen prevented an unrecognized app from starting. Running this app might put your PC at risk.” ○ To bypass this, click “More info.” A new option will appear at the bottom right hand corner of the window saying “Run anyway.” Click this button. ● The computer will ask if you want to allow this app to make changes to your device. Click “Yes.” ● A new window will appear from coralct_installer that says “Preparing for installation. This may take a few minutes…” 5 ● The next window that pops up should contain information on the version of CoralCT and copyright information. Click the blue “next” button once you’ve reviewed this section. ● Next you will select a destination folder. The default location is your applications folder. If you prefer a different folder, click the blue “browse” button on the right. ○ If you’d like, you can add a shortcut to your desktop. ○ Click the “next” button once the appropriate folder is selected. ● On the MATLAB RUNTIME screen do not click anything but the “next” button. ● The license agreement will appear as the next screen. ○ Read through the license agreement, then click “Yes.” ○ The “Next” button should appear, click to move on to the last section. 6 ● The last window asks you to confirm the folder destinations. Click the green “Begin Install” button at the bottom right of the window. ● Allow the program to install. This may take a few minutes. ● Once downloaded, hit the blue “Close” button on the bottom right of the window. Opening Program Creating a Working Directory ● Upon opening the program, a window will prompt you to select a local working directory. This prompt appears each time you start the program. Your local working directory is where all your coral core data is stored on your computer. This includes the CT scan of the core you are working on, CT scan data you choose to save with the checkbox on the main screen, and downloaded growth rate datasets. 7 ● Click the green button labeled “Choose local working directory.” ● Create a folder, then click “Select Folder.” ● You can save your preferred directory so that it will be automatically selected when opening the program in the future, but you may still change it at any time if needed. ● It is recommended to only have at least one local directory folder per user. Creating an Account ● In the top-left corner of the Home Screen, select the “Create Username” button. ● Fill in the fields and click “Register” on the right. ● We’ll get a registration request on our end and activate your account. ● We’ll then send you an email with your username and password within 1-2 business days. ● If you haven’t received an email from us after a few days, please email us at [email protected]. ● Once your account is activated, you can enter the username and password you created and click “Login” on the Home Screen to proceed. 8 Features of Home Screen ● Remember Me? – When checked, your username and password will be automatically filled in. This is not recommended on shared devices. ● Forgot Password? – Click this button to reset your password. Ensure your username is entered into the blue box before clicking. A temporary password will be sent to the associated email account for logging in. ● Change Password – Allows you to change your password. First, enter your username in the blue box, then click "Change Password." You’ll be prompted to enter your current password and the new password. Click "Apply" to save changes. ● Download User Guide – Click this button to download the latest version of the user guide. ● Leaderboards – There are two leaderboards: the overall leaderboard (left) and the current-year leaderboard (right). The "cores processed" refers to entire coral cores analyzed, while "bands processed" represents individual bands within an 15 ■ Choose text color – This button allows you to change the color of the text being imputed. Choose the color before drawing a textbox. ■ Edit annotations – This allows you to modify the text in the textbox and drag the textbox to another spot. When finished, a tab will open to the right of the window. Click “Done editing” ■ Send to server – This button will send the screenshot and any notes you wrote in the textbox to the server. This allows it to be viewed by other researchers. ■ Close window – This button will close the screenshot window. Pressing this before “Send to server” will not save the screenshot. ■ Line measure – This tool lets you measure the entire length of the core or a section of the core. ○ View screenshots – This allows you to view screenshots taken by other researchers. ■ After clicking, it may take a few seconds to pop up. ■ When finished, click “Close window” in the top left corner. 16 ○ Show smoothed bands – By clicking this button, the bands will smooth out to form one cohesive line. ■ The default shows interpolated bands (points that are connected together). ■ The smoothed bands are what will be used for calculations of growth parameters. ■ Make sure the smoothed bands are accurate to where you believe the bands are before processing. ○ Edit smoothing – Use this to make your smoothed bands match the actual bands more closely. ■ You can adjust two filter parameters here: filter width and filter standard deviation. ■ The larger the filter parameters are, the smoother the bands will be. Methods ● Modify Core Image – Use the slide bars and the projection drop down menu on the right side of the screen to make the bands more visible. Try out different settings to see what works best for you. ○ Projection ■ You can choose to view the min, mean, or max projection. ■ This choice determines how the voxels (3D pixels) are projected onto your screen. ■ Mean projection displays the average value of the density for that slice. ■ Min and max displays the lowest and highest density respectively for that slice. ■ The default is the mean projection, which typically works best, but a different projection can be a better choice depending on the core. ○ Brightness ■ This slide bar will adjust the brightness of the core. ○ Contrast ■ This will adjust the contrast or the difference between the dark and light bands on the core. ○ Slice Thickness ■ This changes how many voxels (3D pixels) in depth are used for the projection. Having a thicker slice will make the image look smoother. 17 ■ The slice thickness is shown by the red box in the axial view (bottom right-hand corner). ○ Slice Location ■ This moves the location of the slice forward and back. You can see the location when looking at the axial view of the core in the bottom right corner. ■ For less complicated cores, try to make the slice location central. ■ For more complicated cores, you may only see clear banding closer to the edges. ○ Slice Rotation ■ Because a CT scan is a 3D image, you can use “Slice Rotation” to view the core from different angles. You can see your current rotation by looking at the axial view in the bottom right corner. This feature is not available for X-rays. ■ Before you start making bands, it's important that you look through the different rotations of the core first to find the best projection for you. You will begin in 0°, but may notice an area where the bands are blurred/unclear. Go to 45°, 90°, and then 135° to see if that area’s bands are more distinct before you begin mapping out bands. There is no set rule on what rotation you have to process a core in – do whatever rotation has the clearest bands. 18 ■ You should find a rotation that shows the corallites, which are formed by individual coral polyps, growing upwards (lines) and not into or out of the screen (dots). Upwards Into/out of screen ■ If you find one rotation that has distinct bands throughout the core, you only need to do that one rotation. ■ However, if the core is more complicated (i.e. there is no single rotation without an area of blurred/unclear bands), it's best to complete multiple rotations. Cores with less clear banding may need more rotations to get a clear picture of the coral’s growth. ● If you decide to do multiple rotations, you need to do at least 4 rotations (eg. 0°, 45°, 90°, and 135°). ● Marking a Band – Once you have found the best projection, you can start identifying bands! ○ In order to zoom in to the top of the core, click and drag a box with the zoom button. ■ Don’t zoom in too close. You should be able to see 5-10 bands below the one you’re working on so you can see the banding pattern. 19 ○ In the top left corner, press the button that says “Identify next band.” It should say “Next band will be band 1.” ■ “Next band will be band X” tells you which band you're marking. ○ Your mouse should now be in the shape of a circle, this will allow you to place the tie-points for the line. ○ If using automatic band detection: ■ Click on the center of the band. ■ You have the options to accept or reject the detected band depending on how well the automatic detection worked. ○ If not using automatic band detection: ■ Going left to right or from the middle out, place the tie-points along the band. ○ Be consistent with your band placements. ○ In this example, tie-points are placed in the darkest part of the dark band. ○ Bands could also be placed in the center of the light band or where light and dark meet as long as it is the same throughout the entire core (i.e. do not begin with mapping out the dark bands then switch to mapping the light bands halfway through. Follow the pattern you set for yourself throughout). 20 ○ If satisfied with the band you’ve mapped, click “Done with band.” If not, click “Redo this band.” ■ There is also the “Draw a box to delete clicks on this band in the axial view below” button. More info later in this subsection (See “Modify Bands”). ○ If the core has ambiguous banding, it is up to the researcher to determine where bands are. ○ With the first band done, the system automatically will go to band 2 when hitting "Identify next band.” ○ This process continues until you have identified bands for the entire core. ○ It is okay if the bands become diagonal, have a slope, or do not go all the way across the core, but the bands cannot be completely vertical. If you reach a part of the core where the bands are vertical (usually near the bottom), stop mapping bands. ● Rotating the Core ○ If you decide to do multiple rotations, use the last slide bar on the right side to rotate the core. 21 ○ Once rotated, you should see numbers on the core in yellow. These show where you’ve placed bands on another rotation. ○ At this point, do not click “Identify next band”. It will cause your band number to continue from where you left off at the bottom of the core on the previous rotation. ○ Go to “Jump to band” at the top of the screen. If you wish to start back at the top, type 1 in the box and click “Apply.” ○ This will start the band counting back at 1 in this rotation and you’re free to click “Identify next band” again. ○ There may be more bands at the bottom of the core only visible at certain rotations. It is okay if you do not end with the same number of bands every rotation. ○ There is an option to hide interpolated bands (button located below the core) as well. This will hide the previous band markings. 22 ○ These previous bands become more visible the more rotations completed, eventually becoming partial lines. ■ This can help you place bands if it is hard to distinguish at certain rotations. ○ Once four rotations are complete, rotate the core to 180°. If there are incomplete bands (eg. bands 1 and 3 in the image below), complete those bands. 23 ■ Reminder: You may choose to create bands in either one rotation (2D) or multiple (3D). On a more complicated core, where you don’t have clear banding all in one rotation, it’s recommended that you do multiple rotations (4 rotations minimum). ○ Whether you do one rotation or multiple, it’s important to check your work before submitting. This is especially important if you’re only doing one rotation. ■ Check for bands you may have missed or marked incorrectly by looking at different rotations. ○ After all rotations are complete and you’ve checked their accuracy, click “Process Growth.” ● Modify Bands ○ Draw a box to delete clicks on this band in axial view below ■ When mapping a band, you’ll see an orange button the right side of the screen titled “Draw a box to delete clicks on this band in axial view below.” ■ Click and drag the mouse on the axial view after clicking the button. ■ When released, the points inside the box should disappear. ■ Click “Done with band.” ○ Jump to band ■ This button sets the next band to be identified. Type the band number then click “Apply.” ■ This must be set to 1 when starting a new rotation. ■ If you only need to add a few bands at a certain rotation (e.g. 180°), use this button to jump to the exact band you need. 24 ○ Redo band ■ This button will erase the band number entered into the box. ■ This will leave a space for this band, and it will be the next band to be identified. ■ Be aware that this will redo the band in all rotations. ○ Insert band below ■ This button will insert an empty space for a band below the number entered and shift the following bands up one number. ■ This is helpful if a band is accidentally deleted, or if a band that was not marked becomes apparent at a different rotation. ■ This will reset the “Identify next band” to the number after what was entered in the box. ○ Delete band ■ This is different from “Redo band” in that the rest of the bands shift down a number. ■ This should be used when a band is mistakenly placed and other band numbers need to be corrected. ● Core Breaks ○ Core breaks are used to skip years. In other words, you may want to not measure growth between certain band numers. ○ These can be used if the CT scan or X-ray contains multiple core pieces that are placed next to each other in the image. ○ To edit the core breaks, click “Edit core breaks”. ○ This enables a dialog box and a list of currently added breaks. Type a number into the dialog box and then use the “Add/remove” breaks button to add or remove that break. ■ If the number in the dialog box is not in the list, it will be added to the list. ■ If the number in the dialog box is already in the list, it will be removed from the list. ○ Click “Done with breaks” to return to the main screen. 31 Determining Age ● The year you estimate here indicates which calendar year most of the growth between bands 1 and 2 occurred in. ● To estimate the calendar year of the first band, follow these steps: 1. Find out when the core was collected. This information can be found on the Process Growth page, to the right of the comment box. 2. Go back and estimate how many months of growth are above the first band. 3. Subtract that number of months from the date of collection. 4. If the month you get is January-June, indicate the previous calendar year in the submission box. If the month you get is July-December, write the same year as collection. Example 1: 1. Core T769 was collected in June 2013. 2. The first band is very close to the top with only around two months of growth above the first band. 3. Therefore, the first band must have formed in around April 2013, two months before the core was collected in June 2013. 4. This is only 4 months into 2013 so 2012 is actually a better estimate for this core. Most of the growth between bands 1 and 2 (8 months worth) occurred in 2012. ● Most of the time, the value you input in this box will either be the year the core was collected or the previous year. ○ On occasion there are cores where the estimated calendar year of the first band is two years previous to the collection year. 32 ○ This happens when the core was collected early in the calendar year (January, February) and there is nearly a full year of growth above the first band. Example 2: 1. Core K19 from the Central Red Sea was collected in January 2020. 2. The first band is very far from the top with about 9 months of growth above the first band. 3. Therefore, the first band must have formed in around April 2019, 9 months before the core was collected in January 2020. 4. This is only 4 months into 2019 so 2018 is actually the best estimate for this core. Most of the growth between bands 1 and 2 (8 months worth) occurred in 2018. Final Processing Steps ● Select “Send outputs to CoralCache server” when you have completed filling out the information. ● Check “Delete your previous output files” if you wish for all previous growth processes that you have sent to the server for that core to be deleted. ● Do not check this if you want previous processed data for that core under your username to stay on the server. 33 Submit Data ● It can take some time for your submitted data to become available on the app because the CoralCT team manually uploads and checks each of the scans that are submitted. ● There especially may be delays if the data you submit are not standard. ● To avoid having to wait for us to upload your data, you can directly submit your data to our server (See the “Direct Submission” subsection). Uploading Scans ● Navigate to the Submit Data button (upper right-hand side of the main menu). ● You can upload your CT or X-ray data using the “Submit zipped file”, “Submit data folder”, or “Submit X-ray image file” buttons. ● Uploading CT data: ○ If you are uploading CT data, you can use either the “Submit zipped file” or “Submit data folder” button. ○ We recommend zipping the folder that contains the scans and uploading it using the “Submit zipped file” button. ■ A zipped folder can be uploaded and downloaded faster than one that has not been zipped. ○ The folder or zipped folder you upload should contain many DICOM files. ○ We only accept DICOM files (.dcm). If you have TIFF files (.tif) and are submitting a CT scan, you’ll need to convert them. Refer to the “Converting and Resizing” subsection below. ○ Use the core sample ID to name the file (eg. T769.zip). ● Uploading X-ray Data: ○ If you are uploading X-ray data, you can use the “Submit data folder” or the “Submit X-ray image file” button. ○ Submit a folder containing TIFF files using “Submit data folder” or a stand alone X-ray file using “Submit X-ray image file.” ○ There should be a scale bar included with the X-ray images. ○ Use the core sample ID to name the file (eg. T769.tif). ● Although it’s possible to upload multiple files at once, we recommend uploading one zipped file or folder (i.e. one core) at a time. This will take less time for the person uploading the data and will be more streamlined on our end as well. 34 Uploading Metadata ● Download the metadata template on our website or using the “Get Metadata template” button. ● Row 5 of the template contain notes on what you should enter in each column. ● You should have one row for every file that you submit. ● You can submit one metadata file for every batch of cores you submit or for every region. ● Important details: ○ The name entered into column 1 of the metadata sheet (Sample ID) should match the name of the data file you submit exactly. ○ The latitude, longitude and year of collection are important and required. Be sure to enter them correctly. ● Click “Submit metadata file” and navigate to it in your file navigator. Uploading Standards ● The process for uploading standards is almost exactly the same as the submission process for regular coral cores. ● Uploading scans ○ Each standard piece must be cropped and uploaded as a separate file. ○ You can use the cropping tool described below to crop out each piece of the set of standards (See “Modify Data” subsection). ● Uploading metadata ○ Only the following metadata are required for standards submission: name, region, subregion, genus, owner, hard drive, ct, xray, dpi. ■ All other columns can be left blank. However, do not delete any of the columns from the spreadsheet. ○ When uploading standards, always enter “standards” as the region name (case sensitive). ○ For the subregion, enter either the name of the core that the standards are associated with or the name of the group of standards (e.g. CoreName, StandardsSet1). ○ The CoreID should the the name of the individual standard. Modify Data ● Converting 35 ○ If you’re uploading CT scans and your files are in TIFF format you’ll need to convert them using the “Convert Tifs” button. ○ Click the “Convert Tifs” button and select a folder that contains the individual TIFF files. ○ Then you’ll be asked to enter the following metadata: slope to rescale image intensity, intercept to rescale image intensity, pixel spacing (mm), slice interval (mm), and core name. ○ Hit “Go!” and wait for CoralCT to convert your files. ○ You’ll see a new folder within the folder you selected titled “dicoms.” ○ This folder will contain the converted tiffs. ● Resizing ○ If the coral scan you upload is large you may experience issues with opening the file and lagging when marking bands. ○ Resizing will decrease the resolution but make it a smaller file size that is easier to open and work with. ○ To do this, use the “Resize DICOMS” button and upload a folder that contains a subfolder with all of the individual dicom files. ○ If you upload a folder with multiple subfolders you may encounter an error. In this case, either contact [email protected] or reorganize the folder so that there is only one subfolder, which contains all of the .dcm files. ● Rotating Dicoms ○ CoralCT is designed to use dicom images that look like the one below to create the 3D projection that you see on CoralCT: ○ ○ Sometimes the core is scanned in a different orientation and the individual dicom images look like this: 36 ○ ○ We highly recommend scanning coral cores the standard way to minimize artifacts and get a more accurate scan. Feel free to contact us for more information about scanning cores and what to do if your core was not scanned in the optimal orientation. ○ To be able to upload your core to CoralCT, you’ll need to rotate the DICOMS via CoralCT. ○ Go to “Submit Data” then “Modify Data” and click “Rotate DICOMS: choose a folder containing a subfolder with .dcm files.” ○ Choose the folder containing a subfolder of the dicoms you want to rotate. ○ Indicate how you want to permute or rotate the dimensions. ○ Hit “Go.” ○ A new folder called “rotated” containing the rotated DICOMS will appear in the folder you chose. ● Cropping ○ To crop a section of your CT scan, select the “Crop DICOMS: choose a folder containing a subfolder with .dcm files” button and choose the folder containing a subfolder of the dicoms you’d like to crop. ○ You’ll then be given the option to crop from three different views: axial, sagittal, or coronal. ○ Choose one of the three options and then wait for your CT data to load. ○ Once the image of the core opens, use your mouse to draw a box over the area that you’d like to crop. 37 ○ The cropped DICOMS will appear in a new folder titled “cropped” that is located in the folder that you selected at the start. ○ If you’d like to crop another section from the same file, be sure to move the “cropped” folder elsewhere. ■ If you were to select the same folder again as is, you would get an error because a subfolder called “cropped” already exists in the folder. Direct Submission ● To avoid having to wait for the CoralCT team to manually upload your data, you can directly submit your data to our server. ● For this to work correctly, however, the data submitted need to follow the specifications exactly. ● To do a direct submission you’ll need to submit CT or X-ray data and the metadata associated with the core. You may also choose to create a new map if one doesn’t already exist. ● 1. Select CT scan or X-ray ○ CT scan ■ Navigate to a zipped folder containing the DICOM files of the core you’d like to upload. ■ The folder must be zipped and titled “dicoms.zip” ■ It must contain only .dcm files. The files may or may not be organized into subfolders. Either format is fine. ○ X-ray ■ Navigate to the TIFF file of the core you’d like to upload. ■ The file must be titled “xray.tiff” ● 2. Select completed metadata template file ○ Download the metadata template and fill in the metadata for the file you are submitting. ○ Before you submit the metadata template, it’s important that you delete all rows containing instructions and examples. ○ Only two rows should be submitted: (1) headings and (2) that core’s metadata. ○ Must be a .xlsx file; it can’t be a .csv. ○ Column A, name ■ The core ID, this should be the original sample name. ■ No spaces are allowed, dashes and underscores are okay. ○ Column B, piece 38 ■ If the core is broken and the pieces were scanned separately, indicate the piece number here (e.g. A, Top, CoreName-2). ■ The value entered can't be a single number (i.e. 1, 2). ○ Column C, region ■ This is a large geographic region like a country or body of water (e.g. Taiwan, Red Sea, Eastern Australia). ■ If the region that you want to enter does not already exist (check the dropdown menu on the main menu), you can choose to make a map, which will display while you navigate to the core on the main menu (details on map making later in this section). ■ Standards: ● If you’re uploading standards, enter “standards” as the region (case sensitive). ○ Column D, subregion ■ This is a smaller area within the region selected (e.g. Dongsha Atoll, Central Red Sea, Northern Great Barrier Reef). ■ Again, if the subregion that you want to enter does not already exist (check the dropdown menu on the main menu), you can choose to make a map, which will display while you navigate to the core on the main menu (details on map making later in this section). ■ Standards: ● If you’re uploading standards, enter either the name of the core that the standards are associated with or the name of the group of standards (e.g. CoreName, StandardsSet1). ○ Column E, genus ■ The genus of the coral the core came from. ■ Do not include the species name here. ■ The first letter should be capital (e.g. Porites, Diploria). ○ Column F, owner ■ Enter the username(s) of the user(s) that you want to have full access to the core. ■ If you select a privacy level other than 1 (completely open-access), the usernames you enter in this box will be able to bypass any restrictions. ■ Enter the usernames of any people that should have full access to the core separated by “//” if there are multiple people (e.g. user1//user2). ■ To change the list of users once your core is uploaded, email us at [email protected] or [email protected] ○ Column G, notes 39 ■ Enter any notes and details you’d like to provide about the core. ○ Column H, citation ■ Enter the doi link for a publication associated with this core. ■ Only link one publication. ■ The text entered here should read like this: https://doi.org/1234567 ■ If a publication associated with this core doesn’t exist, leave this box blank. ○ Column I, acknowledgements ■ Enter the names of anyone to acknowledge for the collection or management of the core. ○ Column J, hard_drive ■ Enter 1 as a default. ○ Column K, flip ■ Enter 1 to flip the core if it was scanned upside down. ■ Enter 0 if the core is right-side up. ○ Column L, lat ■ Enter the latitude of the coring site in decimal degrees. ■ Other coordinate formats are not accepted. ○ Column M, lon ■ Enter the longitude of the coring site in decimal degrees. ■ Other coordinate formats are not accepted. ○ Column N, depth ■ Enter the depth from which the core was collected. ■ This needs to be a positive integer and cannot be a range of numbers. ○ Column O, month ■ Enter the month of collection. ■ Do not enter the name of the month, instead provide the number associated with it (e.g. for August, write 8). ○ Column P, year ■ Enter the year of collection. ○ Column Q, file_size ■ Enter the file size in megabytes (MB) of the file you are uploading. ○ Column R, unlocked ■ Choose a number for the privacy setting you would prefer. ■ 1 = fully open to all users. ■ 2 = restricts output data (calcification and extension results after processing). ■ 3 = restrict output data and raw image files. ■ -2 = completely hidden from others. 40 ○ Column S, denslope ■ If you have calibrated the density of your core, enter a slope that conforms to the following density calibration equation here: Hounsfield Units = slope*density + intercept. If you have not calibrated density, enter 1485.5 for CT scans and -99 for x-rays. ○ Column T, denintercept ■ If you have calibrated the density of your core, enter an intercept that conforms to the following density calibration equation here: Hounsfield Units = slope*density + intercept. If you have not calibrated density, enter -768.9 for CT scans and -99 for x-rays. ○ Column U, ct ■ Enter 0 for x-rays and 1 for CT scans. ○ Column V, xray_positive ■ Enter 1 if the x-ray is a positive and 0 if it is a negative. ■ Enter -99 if it’s a CT scan. ○ Column W, xray_dpi ■ Enter the digital pixels per inch for the x-ray image file. This will be used to calibrate the scale. ■ Enter -99 if it’s a CT scan. ● Once you upload both files, click “Submit” ● If the region/subregion does not already exist, you can make a map ● 3. Make a map ○ Click “Make a map” and enter the western-most, eastern-most, northernmost, and southern-most coordinates in decimal degrees of the rectangle that encloses the region/subregion. Include negative signs as needed. ○ ○ Choose a map resolution ■ The higher the resolution, the longer it will take for the map to load in on the main menu when you’re selecting a core. S N W E 47 ● In file explorer, go to your downloads folder. There should be a download called "coralct-install." ○ If you don’t see the file, you can also download the newest version at www.coralct.org and follow the downloading instructions earlier in the guide. ● Double click the file. Click yes on the pop-up asking to make changes to the device. 48 ● After a few seconds this screen will appear ● Click "Next." ○ These will be the same prompts as the initial download. ● Click "Begin Install." ● Reopen the program once installation is complete.