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Tips on screen grabbing scientific images for an electronic lab notebook

Posted by Rory on October 25th, 2010 @ 10:09 am

Most of the images you’ll want to attach to an electronic lab notebook like eCAT  you’ll already have as an image.  Sometimes, however, you’ll want an image of something you can see on your screen, but which isn’t actually an image. A common of example of this is a chart shown in Excel or OpenOffice. It looks like an image, but you can’t export it from Excel as an image. What to do?

There are a variety of things you can do to turn something you see on the screen into an image for upload to an electronic lab notebook like eCAT:

An image on a web page

Right-click on the image (Ctrl-click on Mac), and select “Save image as”.

An image in another application that can export images

Lots of applications that deal with images of one form or another can export them as a standard format such as PNG, JPG or TIFF. Once exported, the image can then be uploaded to eCAT. TIFF is often preferable for scientific images as it can include metadata.

Spreadsheets

Excel does not allow export of charts as images. However, you can add a capability to your copy of Excel which will allow you to export a chart as an image. This is fully described on this web page.

OpenOffice Calc does not allow export of charts as images. However, you can copy the chart and paste it into OpenOffice Draw, which does allow export as an image. Select the chart so it has green handles, copy and paste into Draw, then in Draw while still selected do File | Export.

An arbitrary area of your screen

Sometimes you’d like an image of part of your screen – for example a portion of an image, or a portion of a web page. Different operating systems provide different functionality and applications for this – here are some options:

  • Windows/Vista. Use the PrintScreen button on your keyboard (usually towards the top and right and labelled PrtScr). This will put an image in the Clipboard of what is on your screen. You can then paste this into another program.Or you can use the popular free IrfanView application, downloadable from here . Options | Capture/Screenshot lets you capture the whole screen or a specific window, and then edit it. To select a portion of the image, just click in the window and drag your mouse. Then use Edit | Crop selection to reduce the image to the portion you selected, and finish by saving the image.
  • MacOS. Use the Grab utility, which is located in Applications>Utilities. With the Capture menu, you can choose to capture a specific area of the screen, a specific window, or the whole screen (use Timed Screen). When you save the file, it will be saved as a TIFF image.
  • Linux. Most Linux variants include a screen grab utility, usually under the Applications menu, which will save the screen or a window as an image. To cut out a specific portion of the screen image, the GIMP image editor can be used. Select Tools | Transform Tools | Crop, drag the mouse over the region you want to keep, and press Enter. The image will be cropped and you can save it.

Further ideas on screen grabbing are here .

Once you’ve grabbed your screenshots, you can insert them into a record in eCAT or import them from the dashboard or as a child record.

How to import images from the dashboard and as a child record in an electronic lab notebook

Posted by Rory on October 18th, 2010 @ 10:18 am

Last week I looked at how to insert images into a record in the electronic lab notebook  eCAT.  This week I’ll look at two other ways of importing images into eCAT, from the dashboard and from the record page.

Importing images from the dashboard

To start, just click on the Import menu item and then on Image

You will be taken to the import page, which looks like this:

The import page

You can choose to import images from your local computer by uploading them to the server, or you can import from an attachment store that your administrator has defined for you.

Importing from your local computer

To import from a local file, click “Choose File” or “Browse” (the exact text depends on your browser) and then select the file you want to upload. eCAT supports a variety of image types. The standard common images types are all fully supported – JPEG, BMP, PNG, GIF etc. We also support a range of specific scientific types such as TIFF, Zeiss LSM, Zeiss ZVI, Delatvision, Biorad (.pic) and Metamorph (.stk).

Importing from the local computer

If you wish to remove a file you have selected for upload, then click the red cross beside the file name.

Importing from an attachment store

To import from an attachment store, click the “Import files from attachment stores” button. Then click in a text box that says “Click here to select an attachment”. The following screen will appear.Importing from an attachment store

Select a file to import from the attachment store, and then click “Insert” to add it to list of files to import. You can import more than one file from attachment stores at once by clicking the [+] button to the right of the text box saying “Click here to select an attachment”.

When you have image files selected from either the local computer or an attachment store, click “Import” to import the files. Some image types support a preview and allow selection of the size of thumbnail images you will see in your imported records. If the image type you are importing works this way then you will see a screen similar to the following:

Previewing an imported image

When you have finished selecting the image sizes, click “Save” to save your settings. You will be taken to the target record if you are importing more than one image, or to the record that you have imported if you have imported a single image.

Importing images as children of a record

When you are viewing a record, you can click the “Import” option in the Children section of the main menu on the left hand side.

This will import the image as a child record of the record currently being viewed.

How to upload images to an electronic lab notebook

Posted by Rory on October 12th, 2010 @ 12:48 pm

The thing you’ll probably want to do  most often with images is insert them into a record you’re working on.    For example, here’s what one  user of the electronic lab notebook eCAT wants to do in eCAT — no doubt representative of lots of users:

“Every day, I take a few pictures, so I want to upload the images directly into my[eCAT] field journal.  I want it to have a paragraph of writing, then a few pictures for that day, then another paragraph, then more pictures, etc.  When I’m finished, I want to be able to print out my field journal with the pictures at the appropriate places, all as one document.”

So how do you get images into eCAT to do that?

1.  Images from the web

To insert an image from the web into an eCAT record, you go to the record, click edit, and then click on the ‘insert image’ icon in the eCAT record editor, which looks like this

The following box will popup:

To find the url of the image on the web, right click on the image, select ‘copy image location’, paste that into the ‘image url’ field in the popup box, and select ‘insert image’.  The image will be inserted into the eCAT record you are editing.

2.  Images from your files

If you want to insert an image from one of your files into an eCAT record, just go to the record you want to insert the image into, click edit, and then click in the location you want to insert the image.  Then click on the following button in the eCAT editor to find the file you want to insert:

The following box will popup:

Next, select an attachment store and a file, and click insert.  A link to the image file will be created at the location in the record you indicated, and when you save the edit you have made, a thumbnail of the image will appear at that location.

3.  Getting images into your files and ready for insertion into eCAT

If you want to insert an image from your files into eCAT, you first want to make sure it’s there in your files in a way that eCAT can see!  Here’s a quick primer on ways of getting images into your files.

Personal and Team Hosted versions

If you’re using a Personal or Team Hosted eCAT it’s  easy to get an image file into a place eCAT can see.  Take a look at this page, http://myecat.axiope.com/help.html?page=DesktopStore_Windows, and when you have your folder set up, just drop the files you want to work with in eCAT into the folder.

Install version

If you’re using an Install version, your IT or the person who runs your eCAT server should have already set up ‘attachment stores’.  These are places where you can put  image files that eCAT can see.

Your image files are now visible to eCAT.  To insert them into an eCAT record just follow the simple steps set out in Section 2 above.

How to set up a new lab with an electronic lab notebook

Posted by Rory on October 4th, 2010 @ 9:44 am

I recently  came across a great primer on how to set up and run a new lab.  It’s called How to set up a new life science lab without HHMI funding, and it was put together by some people at Dartmouth to welcome new faculty members.  Their recommendations are simple:

  • You’re the best postdoc you’ll have for many years; stay at the bench
  • Grow slowly and selectively
  • Hire a research associate who is a stable person and not too proud to help you be more productive
  • Submit grants early
  • Compartmentalize and plan your time
  • Balance novel and risky experiments with meat and potatoes
  • Attend just one meeting a year

Hmm, I thought, eCAT can help with each of those recommendations.  Here’s how.

Stay at the bench

Spending time at the bench is one thing when your main focus is your own research, quite another when you have all the responsibilities and commitments that come with setting up and running a lab.  To make time for research, you’ll need to be well organized and efficient in carrying out and  documenting your experiments.  And you’ll need to be in close touch with the research  everyone else in the lab is doing — you’re not on your own or supervising one or two people any longer, you’re leading a group.

An electronic lab notebook can help on both accounts.  Larry Gonzalez  at the University of Okhlahoma summarized nicely how eCAT helps both him and his lab get better organized:

“eCAT  helps keep me organized, and it’s very good at increasing my efficiency in documenting my research.  Myself or a research technician or a post doctoral fellow can generate a protocol and store it in eCAT.  We can create the data forms that can be filled out manually and entered during an experiment, and we can link to external files.  And if someone would prefer to use another program like Excel to generate spreadsheets instead of entering data into eCAT they can create a spreadsheet and we can link to that file, and its all kept together and organized well in eCAT.  And then when an experiment is completed we’re able to export the data to an external statistical data program for subsequent analysis.”

Grow slowly and selectively

An important benefit of a good electronic lab notebook is that it is flexible enough to grow as your lab grows.  In the most obvious way, it should be able to accomodate the addition of new lab members by making it easy to set up new accounts for them.  There are also less obvious things a good ELN can help with, like  having the ability to set up groups of users.   In eCAT you can set up an  ‘all users’ group, with permissions set on what records the members of the lab can view, what records they can edit, etc.  So you don’t have to set up a new permissions regime for each new person who comes into the lab; you just add them to the all users group and it happens automatically.

Another aspect of eCAT’s ability to help integrate new lab members easily is that, as Alex Swarbrick of the Garvan Institute in Sydney pointed out,

“Since everyone uses the same interface, it is easier for new people to understand the way the lab works and to pick up on projects.”

Hire a research associate to help you be more productive

Postdocs have to be self sufficient and multi-talented to survive, much less thrive, so working with someone else who helps manage you and your new lab may take some getting used to.  To develop a good relationship with a research associate and get the most out of them involves not only interpersonal skills; you also need to establish an environment where collaboration and communication takes place as naturally and as easily as possible.

Introducing an electronic lab notebook as the place where everyone in the lab documents and shares experimental data, as well as meeting notes, protocols and other information not only makes your life easier, it also makes your research associate’s life easier.  And that’s crucial because given the explosion in demands on your time that come with runnning your own lab, your productivity is now impacted by your research associate’s productivity.  If they are left to chase bits of information scattered around other people’s paper lab notebooks, in random disk drives, and on personal computers, a lot of their time is going to be wasted.

With an electronic lab notebook, your research associate can have access to all group records, and can set up structures for recording and organizing things like lab protocols that make it easy for them, and you, to find information.  Heather McClafferty, research associate to Mike Shipton at The University of Edinburgh’s Centre for Integrative Physiology, said after the lab had adopted eCAT:

“Having everything tied together under one resource, so results, protocols, constructs, where things are physically, having everything together under one system has just been perfect.”

Submit grants early

Submitting grants early requires organization.  That’s pretty obvious.  What may be less obvious is that organization becomes a bigger challenge, but can also bring bigger rewards, when you are at the head of a group, even a small one like your first lab.  Your research associate and your students can both be useful resources for preparing for grants:  carrying out preliminary research, finding data from previous projects, and researching and preparing applications.  They will do all this much more effectively with an electronic lab notebook.  With an ELN it is easier to share data and communicate about it, data from previous projects is archived and easily searchable, and when it comes time to prepare the application, (a) people are already working in the same integrated environment, and (b) the data needed to support the application is readily available for inclusion into it.

Compartmentalize and plan your time

The organization theme is obviously relevant here.  But how does an electronic lab notebook help?  First, an online ELN like eCAT is accessible 24/7 from any computer with a web browser.  That means you don’t have to set up a specific time to see what others in the lab have been doing.  No need to make an appointment to go over a student’s paper lab book.  Instead, as Alex Swarbrick says, “I can use eCAT to remind myself of recent experimental results without hassling someone in the lab.”  And Alex, and other eCAT users, are free to arrange their time in the way that suits them, rather than having to fit in with arbitrary schedules, or what’s convenient for others.  The result is more time to spend, and to allocate in the way you find most effective.

Balance novel and risky experiments with meat and potatoes

One of the benefits of a flexible ELN is that it allows you to structure your experiments, and those of others in the lab, in the way that best suits your research.  Mike Shipston at Edinburgh put it this way:

“The great thing about eCAT is it’s incredibly flexible in terms of how you can set it up.  For example each member of the lab has their own folders and puts their own experiments within that, but its every easy to put that information together.”

Having a structured record of your lab’s experiments — yours but also everyone elses — means that you are more likely to spot patterns, discrepancies, and problems.  And see the woods from the trees and develop a better sense of what’s risky and what’s meat and potatoes, and why.

Attend just one meeting a year

This is one bit of advice you almost certainly are not going to follow!  The reality is that you’re going to find yourself on the road quite a lot, whether it’s attending a conference or meeting collaborators about a grant proposal or work on a grant in progress.  With an online ELN like eCAT, you can stay in touch with the work that’s going on back in the lab because you can login over the internet and see what people having been doing, in the evening, between meetings, or whenever it suits you.  And with eCAT’s notifications system, you can send and receive messages about people’s research, and even put links to experiments and other records in the messages, which makes it easy to work collaboratively even when you’re on the other side of the world.  So if don’t follow this last bit of advice, and end up attending meetings regularly, with eCAT you will still be able to keep up with other aspects of your lab’s research.