Biological Imaging



The next step after taking your pictures is to upload them from your camera to the network, sort them, delete the bad images, and back up the good images.  This tutorial will take you through that process.

The workflow outlined here might be different from what you are used to, and it might be different from an optimal workflow on your own computer.  It is optimized to move your images safely and quickly using the equipment we have available; but most of the steps outlined here are probably applicable to your own computer and I'd recommend them for use there as well.  This workflow uses card readers rather than a direct camera connection for 3 reasons:

  1. It is safer.  Connecting a cable to your camera opens the camera up to damage.  If the cable or camera are knocked about while they are connected, the pins on the connector in the camera can become bent.  At best, the connection may no longer function; at worst the camera may no longer work.  A camera is at its most vulnerable when the cable is connected, especially on a busy desktop.
  2. It is simpler.  Assuming a card reader is connected to the computer (many computers now have them built-in), you don't have to fuss with a cable, wait for the computer to recognize the camera and perhaps install and operate obscure software to transfer the images.  Also, if you have images on more than one card, it is much easier in most cases to swap them through the card reader as opposed to the camera, where the card slot is often hidden behind a door.  Also, using the card reader does not drain the battery on your camera.
  3. It is usually faster.  Most card readers will read the cards faster than your camera can send them to the computer.


Preparation:  Before you can upload your pictures you need to know if your camera's card can be read in the card reader that is available.  This means that you need to know what type of card your camera uses.

The image to the right shows 4 different types of cards commonly used in digital cameras (there are about 20 different types, with most being physically indistinguishable from these 4 types.  Compact Flash cards (1) are the largest physically, although they do not necessarily hold the most data.  They were one of the first designs used in cameras and are still the standard used in many of the digital SLR's.  Commonly they can be found in sizes up to 32 GB, although larger ones are available.  They also come in a wide array of sizes; a newer standard called UDMA which can transfer up to 45 MB/sec.  Most cards are solid state, but some manufacturers have made tiny hard drives in this format.

The SD (and SDHC) cards (2) are much smaller, yet have similar capacities to Compact Flash Cards.  This is a newer format, derived from the Multi-media Card (MMC).  They can transfer data up to about 30 MB/sec. They are available in sizes up to 32GB, however a new standard, SDXC, will allow cards up to 2 terabytes in size in this tiny physical package! Those cards will not, however, work in current devices just as older devices are not able to use the newer SDHC cards.  The SDHC cards have speed ratings; Class 6 cards can write 6MB/s; class 4 4MB/s and so on.  SD cards have a notch on the case to make sure they are inserted the right way.  Many have a write-protect tab which physically prevents writing to the card or erasing the images.  This can protect your images, but it can also cause frustration when you suddenly can't seem to get rid of images you have already uploaded to the computer.

Even tinier than the SD cards are mini and micro SD cards (3).  These are electronically similar to the SD cards, but in a much smaller package.  They are more often used in cell phones than cameras.  They can be read in many card readers by inserting them into an adapter that physically resembled a regular SD card.  In this configuration they can also be used in a camera that takes SD cards.  Beware of using the same card in two different devices, however as this can cause errors (see formatting, below).

Also pictured is a Memory Stick from Sony (4).  Memory sticks come in a variety of configurations (Pro, Duo, Pro Duo, etc.); few cameras other than Sony use them.

Not pictured are MultiMedia Cards (MMC) and xD cards; the former is an older standard not  much seen anymore; xD cards are used in many Olympus and Fujifilm cameras.



Shown to the left is one of the computers in the research lab with two card readers attached.  Both readers are connected via the computer's USB ports.  The upper card reader red arrow) is for SDHC cards (it will also read older SD cards).  The lower reader (green arrow), attached by cable, will read a variety of cards including Compact Flash, Memory Stick and SD.  This particular reader will NOT read the newer SDHC cards, but other readers like this are available that do.

Look for card readers on the computers on the island in the lab.  These computers, since they have no seats, are best used for uploading data to the network.  From there, you can access, organize and edit the files on one of the two workstations along the wall in the research lab, or use one of the computers in the environmental science computer lab downstairs.


Note:  the steps below are the basic steps needed to upload and organize your images.  For a more detailed workflow that takes advantage of Adobe Bridge see pages 12-18 in



Step 1

Uploading:  The first step is to get your files onto the network.  To do this, choose one of the computers with a card reader attached.  These are normally the computers on the island in the research lab, although at times we may move a card reader down to the Environmental Science computer lab.

Carefully place the card in the appropriate slot, in the appropriate direction.  Be careful and never force the card (different readers have different configurations; one may accept a card face up and another face down, so it's impossible to write a general instruction).

  1. Start up My Computer on the computer and find the drive with the card inserted (often it will change to the name of the camera brand you are using).  
  2. Hold down the control key and click on the up arrow on My Computer.  This will open a second window.  In the second window, navigate to the scratch drive (usually S: in the lab).  Arrange the two windows side-by side.
  3. In the first window, navigate through the sub-directories until you find the image files.  Press Ctrl-A to select them all. Then press Ctrl-C to copy them all.
  4.   In the scratch directory, navigate to the directory you created for yourself (use your name to name the directory).  You may want to create a sub-directory for each batch of images; the date makes a good name for the subdirectory.  Open the subdirectory and press Ctrl-V to paste the files into that directory.
  5. Some cameras will create images in more than one directory; be sure to examine all subdirectories on the card and copy all of the files using Ctrl-A / Ctrl-C /Ctrl-V as shown in 3 and 4 above.
  6. Remove your card from the reader and put it back in the camera.
  7. Move to another computer, such as the two workstations in the research lab or one of the computers in the environmental science lab downstairs.




Step 2

Sorting:  The next step is to sort the images.  In the labs you can use Adobe Bridge (right); if you do not have Bridge you may want to download the freeware software FastStone Image Viewer (below).  The first pass at sorting involves using the slide-show view of either program to place your images full-screen on the computer.  As you go through them (page up or page down will allow you to advance), eliminate any images that are clearly out of focus or poorly exposed.  Getting rid of bad pictures now saves you work and disk space later on.  To delete an image hit the delete key while it is on screen.  Depending on how the programs are set up, FastStone will ask you if you want to delete the file; if you do it will be placed in the recycle bin (from which it can usually be retrieved, unless someone empties the bin).  By default, using the delete key in bridge simply marks the file "reject".  After you are done with the slide show, sort the files by rating (View:Sort:By Rating) which will group all the rejected files together.  Select them and hit the delete key again to send them to the recycle bin.


Step 3

MetaData:  If you are using Bridge, it is easy to edit the metadata that accompanies each image.  Either use a template (see page 15 from ELM book chapter on Photoshop) or select the metadata pane and manually enter the data.  To do this, first select all the files the metadata will apply to - for instance, your copyright information should go on each image, while location data will vary between images.  

You should at least fill out the creator field with your name; you probably should fill out the copyright field with your name and the year as well (see below left).  Subject information is usually covered in the keywords field; you can enter a number of keywords. 


Step 4


The server is only a temporary storage place.  Please remember that the server could be cleaned at any time.  Therefore, please protect your images by backing them up:


1.  Back them up with a thumb drive.  Insert a thumb drive and copy the files, using My Computer or Windows Explorer from the server to your thumb drive.  NOTE:  NEVER copy files by opening them in a program such as Word or Photoshop and then saving them in a new destination.  This is really stupid for so many ways it's hard to list them all.  Use explorer or my computer.


2.  Burn them to a DVD.  DVD's cost about 25 cents each if you buy them in bulk.  Do so, and use the NERO Burning ROM software on the computer to copy them from the network to the DVD (it might be a good idea to copy them to a directory on the computer's hard drive first, then erase that directory).  You should always close the DVD - you won't be able to write to it again, but you won't be able to screw it up and lose your pictures, either.  Remember, it cost you 25 cents.  Use a marker to write your name and the date on the disk, along with what is on it (Such as "Photos - January 2009).  If you somehow mess up, lose or erase the images on the server you can always go back to the ones on the disk. 


Step 5


The card you put back in your camera still has the images on it.  Once you have them safely copied onto a DVD it's time to get rid of them so you can take more images.  You COULD simply delete all the images, one by one or as a group, but in the long run you will end up with a corrupted card if you do this.  Much better to reformat the card using the controls on your camera (NEVER reformat in the computer as the format will not be optimized for your camera).  Many cameras have both a quick format and a low-level format.  The quick format simply removes the directory that tells the computer where the files are at.  The actual files remain on the card and you might be able to retrieve them later with disk-recovery software which is widely available.  The low-level format removes the directory and the files.  I prefer to use the latter so that the card is optimized to take new images.  If you have backed your earlier images up properly, this is fine.  Most cameras do a low-level format in less than a minute.

Formatting is particularly important if you move a card from one device to another; say from your cell phone to a camera or from one camera to another.   To avoid problems, you should always format a card when you put it in a device (even if it has been used in that device before); just remember that FORMATTING REMOVES ALL FILES FROM THE CARD - so make sure you have things backed up first!


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See some of the imaging equipment we use in our new facilities.


Updated 01/18/09 by DMC