Do It Yourself: Lab Notebook Archiving Project

A while back, the lab moved to an electronic lab notebook (details here and here). One of the drivers for this move was the huge number of hard copy lab note books that had accumulated in the lab over >10 years. Switching to an ELN solved this problem for the future, but didn’t make the old lab note books disappear. So the next step was to archive them and free up some space.

We access the contents of these books fairly regularly so archiving had to mean digitising them as well as putting them into storage. I looked at a few options before settling on a very lo-fi solution.

Option 1: call in the professionals

I got a quote from our University’s preferred data archiving firm. The lab notebooks we use have 188 pages and I had 89 to archive. The quote was over £4000 + VAT for scanning only. This was too expensive and so I next looked at DIY options.

Option 2: scan the books

At the University we have good MPDs that will scan documents and store them on a server as a multipage PDF. There’s two resolutions at which you can scan, which are good-but-not-amazing quality. The scanners have a feeder which would automate the scan of a lab book, but it would mean destroying the books (which are hardbound) to scan them.

I tried scanning one book using this method. Disassembling a notebook with a razorblade was quite quick but the problem was that the scanner struggled with the little print outs that people stick in their lab books. Dealing with jams and misfired scans meant that this was not an option, and I didn’t want to destroy all of the books either.

Option 3: photography rigs

Next, I looked at book scanning projects to see how they were done. In these projects, the books are valuable and so can’t be destroyed, but it must be automated… I found that these projects use a cradle to sit the book in. A platen is pushed against the pages (to flatten the pages) and then two cameras take a picture of the two pages, triggered in sync using an external button or foot pedal. An example of one raspberry pi-powered rig is here. Building one of these appealed but would still require some expense (and time and effort). I asked around if anyone else wanted to help with the build, thinking that others may be wanting to archive their notebooks, but I got no takers.

Option 4: the zero-cost solution!

Inspiration came from a student who left my lab and wanted to photograph her lab books for future reference. She captured them on her camera phone by hand in a matter of minutes. Shooting two pages of a book from a single digital camera suspended above the notebook would be a good compromise. Luckily I had access to a digital camera and a few hundred Lego bricks. Total new spend = £0.

I know it looks terrible, but it was pretty effective!

I put the rig on a table (for ergonomic reasons), next to a window and photographed each book using natural light. It took around 10 min to photograph one lab book. I took the images over a few weeks amongst doing other stuff so that the job didn’t become too onerous. I shot the books at the highest resolution and stored the raw images on the server. I wrote a quick script to stack the images scale them down 25% and export to PDF to make an easy-to-consult PDF file for each lab book. Everyone in the lab can access these PDFs and if needed can pull down the high res versions. The lab books have now been stored in a sealed container. We can access the books if needed. However, having looked at the images, I think if something is not readable from the file, it won’t be readable in the hard copy.

Was it worth it?

I think so. It took a while to get everything digitised but I’m glad it’s done. The benefits are:

  1. Easy access to all lab books for every member of the lab.
  2. Clearing a load of clutter from my office.
  3. The rig can be rebuilt easily, but is not otherwise sitting around gathering dust.
  4. Some of the older lab books were deteriorating and so capturing them before they got worse was a good idea (see picture above for some sellotape degradation).

The post title is taken from the LP “Do It Yourself” by The Seahorses.

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