There are also two videos that might help if you need to set-up or re-configure the system further

Museum of TTU's How To use the camera, stack photos, and operate the software for the SCAN project [Text and photos are from Visionary Digital, Megan ...
Author: Holly McDowell
1 downloads 0 Views 2MB Size
Museum of TTU's How To use the camera, stack photos, and operate the software for the SCAN project [Text and photos are from Visionary Digital, Megan Leber, Lisa Highsmith & James Cokendolpher. tm Except for copyright held by Visionary Digital , the remainder is in the public domain]

The photo above is all the hardware that this system involves. For everything to work properly everything must be plugged in and powered. [photograph modified from: http://www.visionarydigital.com/IntegratedSystems3.html].

Please see the excellent pdf on parts, set-up, and using the Passport system: http://www.visionarydigital.com/vis_dig_manuals/Passport%20II%20+%20VD%20Passport.pdf That pdf will touch on several important points that are not mentioned here (e.g., Dwell Time, overlap of images in stack- calculated steps). Please also see: http://www.visionarydigital.com/vis_dig_manuals/k2_measurement_tutorial.pdf for further details

There are also two videos that might help if you need to set-up or re-configure the system further. Part I (unpacking) www.youtube.com/watch?v=TlbFR-dy4Ic, Part 2 (plugging it all together) www.youtube.com/watch?v=A7KfJ5tvO34

The following manual is IF all of the set-up has already been done, including installation of the software: VD Passport, EOS Utility, Helicon Focus, Photoshop CS extended. Although the length of this document will scare most at first, you will find it overly detailed step-by-step instructions with many photographs Step 1: Turn on all of the components:  laptop [Origin computer and cooling pad fan]  Canon EOS 5D camera (turn it to the option above the on switch)



ST-E2 Speedlite Transmitter (turn to the middle setting, which looks like a vertical line)

 

the (2) modeling lights the (2) 430 EX II Speedlite "Slave lights"  make sure that the two "slave lights" are set to be "slaves" to the transmitter  One should be set to "B" and the other "C";  the transmitter in the middle is always programmed as "A"  If for some reason they are not showing up as "slave lights" hold down the ZOOM button until they do.

Step 2: Open EOS utility and VD Passport software; you need both to take the pictures and to move the camera up and down the focusing rail. IMPORTANT! For EOS utility to work the camera must already be turned on. Once VD Passport is open click "take pictures"

when all elements of the camera are on, the windows will look like this:

Step 3: Prep [clean any dust with camel-hair brush, forceps, or air puffer] the specimen for its photo shoot and place it under the camera [various mounts to hold pins are available- we use a tiny ball of white putty/clay] 

Click on "Live View Shoot" to see what the camera sees  center specimen directly in the middle of the Live View, leaving empty space evenly on each side of the specimen  the grid display on the Live View will help

Note 1: Remember that the image will become inverted in the screen of the camera because the camera isn't facing the same way you are. So if you face a specimen to the left it will appear to be facing right in the camera's lens. Make sure you have it the way you want in the view of the camera before you start shooting. You can with extra effort and time rotate photographs with Photoshop software, if the need arises. Note 2: Take photos of all body views (dorsal, ventral, lateral) at the same magnification. With practice you will note that some specimens are taller than long, so it will be better to take the lateral view photo first to set the magnification for all shots.

Step 4: Focus your image (use 50mm or 65mm based on the specimen size; larger specimens will use the 50mm, smaller the 65mm) 

Manually adjust the magnification on the lens to 50mm macro or 65mm macro  the 65mm zooms to 5x mag, for very small specimens; the camera will be extremely sensitive to movement on the table/camera stand, with the higher magnifications

  

make sure that the magnification on the camera lens matches that shown on the VD Passport make sure that the F Stop in VD Passport matches the "F" on EOS utility. make sure that the Lens in VD Passport is the same that you have on the camera

 

all of the settings in VD Passport depend on the F stop, magnification, and the size of the camera lens. You HAVE to check these every time before you start shooting use the "up" and "down" buttons on VD Passport to move the camera up and down the focusing rail to find the "high point" (the first part of the specimen that comes in focus) and the "low" point (the last part of the specimen to go out of focus)



the "Live View Shooting" image might be a little hard to see in detail if the specimen is poorly lit on the camera stand. Move modeling lights closer to increase light hitting the specimen. Move flashes or diffusers as needed.  as you are moving up/down the rail stop periodically and do a "test shooting" and it will show you how that image will look with the flash



 

do this until you find the highest point of the specimen. Depending on which view you are doing: lateral, dorsal, or ventral, the highest point will be different once you get to the highest point of the specimen in focus click "start here" on VD Passport once you have found the lowest point of the specimen in focus click "stop here"



Note: you might need to re-center the specimen once you find the lowest point to make sure everything (appendages or armament) is still in the frame.

Step 5: Check that the settings match, F stop, and camera lens, and then hit start on VD Passport



the camera should automatically move up to the "high" point you set earlier and then go down, taking a series of photographs, until the place you had set it to stop



Note: If for any reason you need to stop the photo taking process once you have already started it just hit "STOP" on the VD Passport menu

Step 6: you can change the settings within the EOS 5D Utility Program for the camera to fit the purposes of the project.

    



the M means manual focus, you can change it to autofocus on the side of the camera lens (for the 50mm lens) F stands for f stop the lightning symbol stands for the flash, which you can turn off by double clicking the icon the circle inside of the square is for selecting the type of focusing screen shown, you can change this by double clicking the icon the middle button on the bottom portion of the menu, which in the example is RAW + L, tells you what type of picture format the camera is taking  You change this by double clicking on the icon  the available formats are RAW, RAW1 and RAW2. The software can save these RAW images as a small, medium, or large, and JPEG quality; or any combination thereof. You can also change the quality of the JPEG in that menu as well The computer icon (if selected) is just indicating that the images are being sent to the computer and not to the memory card of the camera (which is what we want)

IMPORTANT!: On the 50mm, the lens' magnification is printed in the clear plastic rectangle on the body of the lens, NOT in the camera itself 

i.e., when zooming the camera lens completely, the lens will read "1:1" but in the clear plastic rectangular base on the body of the lens the scale mark will be "1:2"; use the measurement shown in the rectangular window

Step 7: Once the pictures (RAW+JPEG) have been taken they automatically go to the LR WATCH folder on the C Drive.

 

Note: make a folder inside of LR Watch and put the RAWs (CR2) inside it name the folder as the TTU barcode of the specimen. Example: TTU-Z_(then the 6-digit number)

Step 8: once you have isolated the RAWs from the JPEGs in subfolders, open Helicon Focus



Once it is open it should look something like this

 

Note: This is what Helicon Focus looks like when you have nothing inside the LR Watch folder

all of your pictures will show up in the second column under the yellowish colored folder  you should place the RAWs inside a separate folder and use the JPEG for processing

Step 9: starting with the top JPEG in the folder, right click and choose the select all 

this will only work if the only JPEGs in the LR Watch folder are from this specimen

Step 10: Once all the images have been selected click on the second tab on the top left corner named Parameters



The screen should now look like this. The pictures you selected will be in the top right column under the word run.



Note: You want the parameters to be Method C (pyramid) with Full resolution.



If the parameters are correct all you have to do is click Run

 

the photos will now align and stack on top of each other the final in-focus composite image will appear in the bottom half of the screen once it is completed



if it looks good go to the bottom right corner (under output) and right click on the link to save the composite image



Note: we typically name it whatever the TTU number is, that it is combined, and the view it is showing. So, for example, something like TTU-Z_000001_combined_dorsum

 

save it inside the folder that has the RAW images then go back to the LR Watch folder and delete all of the other JPEGs (make sure not to delete your end result if you didn't already place the JPEG inside the folder with the RAW images)

Step 11: open Photoshop CS extended



Once open it should look like this:

 

Once Photoshop is open go to File ( top left of the screen) and go to Open Now go to LR Watch folder and click to open the combined JPEG image that you made in Helicon Focus



it should look something like this (except your photos and folders will be there)

Step 12: once the image is open go to the Image tab and select analysis 

click Set Measurement Scale



once you have done that you just find the one that matches the magnification and lens that you used to take the photographs in the first place.



Note: You must know what lens and magnification you used when you took all the individual photos or the scale will be wrong for the picture.

Step 13: Once you have set the measurement scale go back to the image tab  

go down to analysis, click place scale marker.



Note: You have to set the measurement scale before you try and place a scale marker.

  

if done correctly the screen above should come up you should change the font size to be 30 pick black or white for the color you what the scale bar, and whether the 1 mm will be written under or above the scale bar. Use white bars on dark backgrounds and black on lite backgrounds. We set text below the bar click OK



Step 14: Once the scale is in the photo you can move it around until you are satisfied with its placement. We place the bar on the lower left side. Then go to file, save, and then save the image 

note: save a copy in the Photoshop format (PSD) for future editing, and save in JPEG format, overwriting the stacked photo from Helicon Focus

Step 15: Once it has been saved you can exit Photoshop and return to the LR Watch folder

  

Double click on the folder you created earlier All of the RAW (CR2) images and the one combined image (JPG) should be there, plus the PSD file create a new folder and name it the view that all of these pictures are displaying (dorsum, lateral, or ventral)



Once you have named the folder place all of those RAW images and the two combined images inside that folder.

Congrats! You have now finished one view of one specimen. Repeat these steps to finish the other two views of the same specimen. Then repeat for all new specimens.

Suggest Documents