Tuesday, January 27, 2009

Image download problem fixed

Lately, many Botanicus users have been experiencing difficulty in downloading individual images from the site. This has been happening particularly when users have attempted to download the high quality versions of the images.

We wanted to inform you the users that the problem has now been fixed, and you should not have any further trouble in saving images from Botanicus. However, if you do still come across this problem while using the site, please let us know.

We apologize for the inconvenience this may have caused anyone, and we greatly appreciate your patience while we resolved the issue.

Mike Blomberg
Imaging Lab Coordinator
Missouri Botanical Garden

Friday, January 23, 2009

What is a JP2 file?

"What is a JP2 file? And what do I do with it after I download it from your site?"

These two questions arise frequently with users of Botanicus, so we thought we would make a blog entry to address the topic.

JP2 is the file extension for the JPEG2000 image file format. Think of it as the next generation of the more commonly known JPEG file format. It was introduced in the year 2000 (hence the name), and in principal, it's very similar to JPEG in that they are both compressed image file formats. Because of the compressed file size, JPEG's have long been one of the web standards for displaying images and graphics. The major downfall to JPEG images is that the compression has a negative effect on image quality. The more an image is compressed when saving a JPEG, the smaller the file size will be but also the more the quality deteriorates. JPEG2000 files on the other hand can be compressed to much smaller file sizes with far less deterioration in image quality, which makes it an ideal format for us to serve images to the users of Botanicus.

JP2 files, however, have a disadvantage of their own. Many software authors have failed to embrace this new format yet, and thus programs have been slow in development to offer the ability to open the files. This creates a bit of a challenge for Botanicus users who want to view the files locally on their computer after downloading... Luckily there are four options we recommend for opening JP2 files (three of which are free):
  • IrfanView - A freeware image viewer with limited image editing capabilities.
  • Adobe Photoshop - Current versions offer support for JP2 files, however you will need a plug-in to open JP2 files in older versions.
  • MrSID Decode - A free utility available for download from Lizardtech that allows for the decompression of JP2 files to TIF files.
  • ExpressView browser plug-in - A free downloadable plug-in also available from Lizardtech for standard browsers (including Safari for Mac users) that allows JP2 files to be resaved to other more readily usable formats (JPEG, TIF, etc.).
There are numerous other options available as well (especially as support for JPEG2000 files continues to grow). For more information on other programs that can open JP2 files, please visit the "Application support" section of the Wikipedia entry for JPEG2000. There you will find an extensive list of other popular programs that currently support the JPEG2000 file format.

Mike Blomberg
Imaging Lab Coordinator
Missouri Botanical Garden

Wednesday, October 08, 2008

One million pages!

Today we passed an important milestone in the life of Botanicus. Overnight we published our one millionth page!

It has been a pretty amazing journey getting to one million pages. Botanicus started years ago with a vision and humble beginnings. Scanning for Botanicus started with one single black and white Indus 5001 scanner and somewhat of a makeshift database in which basic information was entered about the books being scanned. Since then Botanicus has grown and changed in ways that even we never imagined that it would! The procedure of getting a book online is now a streamlined series of events that requires little action on behalf of the imaging, library, or information technology (IT) staffs. Thanks to the efforts and innovations from our staff members in these various departments, this streamlining has increased our output well beyond what we thought was possible years ago at the beginning of the project! Our staff that is actively working on Botanicus has grown and currently includes six full-time imaging technicians, two library staff members, and two members of the IT department as well with the assistance of countless others in these departments. We have five full-color book scanning stations (three Indus 5002 scanners, one Kodak i280 sheet feed scanner, and a Better Light copy stand setup) that lately have all been running full shifts five days a week. This is certainly a far cry from our humble beginnings of that single black and white Indus 5001 scanner being used for Botanicus scanning!

Even the Botanicus website itself has evolved into a robust, user-friendly wealth of knowledge… The feedback we have received from the users of the site has proven to be an invaluable resource and has helped to shape the development of the site. Of course, we expected the site to be helpful to people around the world, but again, our expectations have been far surpassed at this point in time! Excitingly, our efforts are no longer limited strictly to just our own website. For example, we now have thriving contributing partnerships in which we share our imaged material with organizations such as the Biodiversity Heritage Library (BHL) and the Encyclopedia of Life. The Botanicus site was always intended to serve the public in general as a free resource of botanical information, but it is interesting to see not only the user hit counts but also the demographics of the site continue to grow over the years. Users of Botanicus are not limited to just botanists and come from all walks of life (artists, historians, medical researchers, etc.). The expanse and impact that Botanicus has had and continues to have is nothing short of astonishing!

Many thanks are due to everyone involved in this project. This includes the library staff, the imaging technicians, and the people in our information technology department who have worked on the Botanicus project over the years. Without the diligent efforts and hard work of these staff members, Botanicus certainly could not have been the success that it has become. Thanks are also in order to the Mellon Foundation and the Keck Foundation without whose financial backing Botanicus would not even have been possible. And last but not least, we would also like to thank you the user for continuing to be active participants in the project (whether you realize it or not). The fact that you use the site and take advantage of the knowledge that is presented makes the entire project worthwhile. Without your support and feedback, there would be no purpose in the existence of Botanicus , and you have proven how important a project of this nature is to the world!

Next stop: two million pages!

Mike Blomberg
Imaging Lab Coordinator
Missouri Botanical Garden

Tuesday, September 30, 2008

The Temple of Flora

Published in 1799, Dr. Robert John Thorton’s masterpiece The Temple of Flora remains an awe inspiring work of botanical and artistic literature even in this modern day and age. After inheriting great wealth from his family and inspired by the work of Carl Linnaeus, Thorton set out to produce England’s finest piece of botanical literature to date. Hiring some of the most skilled artists available at the time, Thorton began embarking on this endeavor, however, after some time he unfortunately he ran into endless problems in getting the work published. Due to social, political, and financial factors, he was forced to trim The Temple of Flora down to just a fraction of his original vision for the project. His determination to have this work published left Thorton completely broke at the time of his death, however, his legacy continues to live on through the exquisite The Temple of Flora. Filled with lavishly beautiful full color illustrations, botanical information, and even nods to classic poetry, The Temple of Flora is truly without a doubt one of England’s premier pieces of botanical literature.

Thanks to the publishing company Taschen Books, this extremely rare work is now available to the general public as a set of high quality large format prints. Packaged in a presentation case, the 110-page offering features a 44-page booklet including author Werner Dressendörfer’s introduction as well as the texts of all 31 botanical plates and 33 loose-leaf Elephant folio-sized color prints for browsing or framing. For a preview of Taschen’s publication of these plates, follow this link:
The Temple of Flora @ taschen.com.

The Temple of Flora is also available through Amazon.com at the following location:
The Temple of Flora @ amazon.com

Mike Blomberg
Imaging Lab Coordinator
Missouri Botanical Garden

Thursday, September 25, 2008

An attempt at reprinting scanned material

Recently, we decided to try to reprint a book that we had scanned. We had been interested in trying out the services of Lulu, an internet website that allows users to self-publish their own works by uploading content and having it professionally printed out in quantities as low as just one. The book we ultimately decided upon was Culpeper's English physician and complete herbal. It is a popular title with both text and some interesting line drawing illustrations. We were hoping to try a book with nice full-color images to see how they would translate to a printed page from a modern day 4-color press, but in the end, we still decided that this would be the best book to give printing with Lulu a test run with.

There were some seemingly minor technical issues that we had to deal with before we could actually send the book off to be pressed. In an idea world, it would be great to just send a PDF file of the book as-is and not have to worry about anything. The reality of the situation, however, is that Lulu only offers a certain number of sizes, and we were going to have to resize all of our images in order to meet the criteria for one of these sizes.

Resizing all of the images seemed like a simple enough task. The pages seemed to be about 6.5” x 9.5” (16.5 cm x 24.1 cm) in size, and the closest size that Lulu offers is 6” x 9” (15.2 cm x 22.9 cm). Logically, it made sense to just shrink every page slightly to fit within these dimensions. I created an action using Adobe Photoshop that would automate this process. After running this automated action, I then created a new PDF of the book that would be uploaded to Lulu’s server and be ready for printing.

Then the problems began… I still am not sure exactly what the issue was, but I had a terrible time trying to upload this file to Lulu’s server. The PDF file was about 350MB in size, but for over two weeks, I could not get it to successfully upload. I would check on the progress of the upload from time to time, and I noticed it would always start over. Sometimes it would upload a small portion of the file and then stop, which in turn left numerous incomplete copies in our Lulu account. I was not sure if the problem was with Lulu’s server or perhaps our own Internet service, so I even tried to upload the file from home, but I still could not get it to work. Finally after a couple weeks of frustration (and determination that eventually it would upload successfully), I spoke with a representative at Lulu who also could not figure out what was going on. She suggested that I try it once more and see if it works, and if it did not, we would proceed from there. By this point I didn’t have much faith in their server. I still had quite a few of the incomplete attempts present in the available files for our account. I decided to try once more from scratch and deleted everything in the process before attempting to upload again. Afterwards I uploaded the file from home without any problems. Success!

We were excited to receive the book in the mail about a week later, especially after all the technical issues we had in getting the PDF for it uploaded. Just looking at the book, one can see that Lulu does excellent work. We chose a paperback binding, and the book looked very professional. Flipping through, however, we noticed some problems… Many times text would run into the gutters. In other instances (particularly towards the end of the book), text would be cut off at the top or the side. After digging a little deeper and figuring out what caused this, I discovered that the Photoshop action I used was inherently flawed. Because of the way we scan the books, the cropping on pages as we’re scanning them can be a bit inconsistent. Using the Photoshop action I created, this inconsistency in the size of the images ultimately led to the text getting cropped when printed. It was a very important lesson to learn should we decide to do something along these lines again in the future…

All in all, we were satisfied with the quality of Lulu’s printing and the turnaround time. My only complaint that I really had with Lulu was in the difficulty of uploading the PDF file to their server. Everything else that we were unsatisfied with (text running into the gutter, text being cut off at the edge of pages, etc.) were due to our own technical errors in preparing the material. I have never had to work on material in a prepress manner like this, and in the end, I found this to be a very interesting learning experience!

Mike Blomberg

Imaging Lab Coordinator

Missouri Botanical Garden

Friday, April 18, 2008

New Changes in the Imaging Lab

It's been awhile since our last blog entry, so we thought we would update everyone on our daily scanning operations...

Exciting stuff has been going on in the imaging deparment! We recently hired three new imaging technicians bringing our total to six, which is the most we've ever had. (Previously, the most we ever have had was five...)

In other news, we have put our Better Light scanning station back into full-time production. This was a major station used in the scanning of large rare books for the Illustrated Garden website. It is a large copy stand setup comprised of a Cambo large format camera and a Better Light scanning back and is surrounded by four hot lights. Once we shifted our focus to Botanicus, this station had unfortunately fallen more and more out of use in favor of the rapid scanning we were achieving with the Indus book scanners. The Better Light produces far better quality scans than the Indus scanners, however, its major drawback its speed. (Since it is a scanning back the imaging sensor moves across the back of the camera much like how a flatbed scanner operates, which in turn creates long scan times as opposed to the instant capture of a CCD in a digital camera.) The good news is that we upgraded to a newer model of Better Light scanning back which is much faster both in scanning speed and data transfer speed, so using the Better Light scanning station as a full-time production station for Botanicus station is much more feasible than before! This station will be useful in adding what we consider "oversized" material (books that are too large to be scanned on the Indus book scanners), so expect to see an increase in the number of folios that are added to Botanicus in the future...

We have also been taking steps lately to further improve our image quality. Every scanning station has undergone calibration methods so that our image captures can be as close to the original as possible. The major drawback to calibrated systems is that the monitors of the end users of Botanicus are not calibrated, so the difference to the average user may not even be noticeable. However, for archiving purposes, it is reaffirming to know that our stored images are more accurate to the source material than ever before in the past.

Mike Blomberg
Imaging Lab Coordinator
Missouri Botanical Garden

Friday, September 14, 2007

Discovered Bibliography by Scientific Name

We've released new functionality in Botanicus to allow users to search across all the scientific names we've indexed throughout our digital library and view a bibliography of occurrences - what we're tentatively calling a "discovered bibliography". To view in action, begin here:


You can search by any taxonomic name, such as Poa annua, or Poaceae, to return results.

Next steps will be to allow users to search for a taxonomic name & return results for it and its synonyms, or taxa below. But before implementing that advanced functionality, we'd like to make sure this works well for a single taxonomic name. Please give it a try and leave comments below. --Chris Freeland