Tiki Goddess

 

Below is the small version. Click here for full size 

 

 

The full size version is 8.8 Mb, JPEG quality 10 saved with Photoshop CS ...  

download and view in Photoshop or a photo editor or use the web browser zoom tool to zoom up).

 

 

Tiki Goddess is a trichrome stained frontal baby mouse tissue section. The slide was purchased years ago (circa 1993?) from Carolina Biological Supply (http://www.Carolina.com), which unfortunately no longer lists this or similar slides (or their web site & web search engine is so pathetic that I cannot find it). Tiki Goddess is also the name of a drink (search www.google.com for recipes). She was named Tiki Goddess because the original headless scan was called Tiki God. I've asked several developmental biologists and/or anatomists whether Tiki is a she or a he. Apparently the key reproductive organs did not make this tissue section. In the future, I might end up with research specimens whose sex will be known. 

 

The current Tiki Goddess was scanned by Microtek representatives during a visit to my office at CHLA, January 2004. They brought their modified Microtek 4000tf/PathScan and Meyer Instrument PathScan Enabler III and scanned in several of my favorite slides while discussing biomedical imaging applications of the 4000tf/Enabler combination. Please note that the modified 4000tf is required to use the PathScan Enabler III adapter. You can find standard 4000tf's for much less than Microtek charges for the modified scanner, but you will need to bite the wallet and spend the money. Yes, I could have scanned it in myself at CoH, but wanted to acknowledge the reps help (I'd name them, but am concerned that releasing their names might cause them to get lots of love/hate email). 

 

The current Tiki is is a reverse Marie Antoinette. The original Tiki Goddess (see http://home.earthlink.net/~geomcnamara/Tiki_Goddess_50percent.jpg) did not have her entire head. In August 2005 I was showing full size Tiki to a colleague and realized the top of her skull was missing. That weekend, I was looking through a storage box and found the CD Microtek had sent me in January 2004 (I had also rescanned Tiki at CHLA and CoH, but never thought of the top of the skull). I'm pretty good with Adobe Photoshop CS but decided to leave the horizontal line in Tiki's head in the interest of letting people see how she was stitched together. I did contrast adjust the image (practically whiting out the background with Adjust - Levels) and erased (made RGB = 255,255,255) the outside, to both reduce JPEG file size and make Tiki appear directly on the web page. 

 

The trip the Microtek reps made to CHLA led me to purchase a modified Microtek 4000tf/PathScan and Meyer Instrument PathScan Enabler III for City of Hope's CITI division. Susan Chao (CoH volunteer, Spring 2005) and I started scanning in histology slides as soon as it arrived (4/2005). We purchased TWO Enabler III's so that we can load the next set of slides while scanning. We use the Microtek software, because Hamrick's VueScan ($40) causes unpleasant grinding sounds and I'm not willing to deal with writing a justification letter for LaserSoft's SilverFast Ai since the Microtek ScanWizard software gets the job done. 

 

I originally posted a version that was scanned at 4000 dpi using SilverFast Ai 5.0 (in Adobe Photoshop) on a Polaroid SprintScan 4000Plus 35 mm film slide scanner, equipped with a Meyer Instruments PathScan Enabler microscope slide scanner (see http://www.meyerinst.com/html/oem/pseiii/default.htm and further information below). The length of the tissue section was >36 mm, so two scans were performed and the head and body merged in Adobe Photoshop 6.0. The current high resolution Tiki Goddess image was saved with JPEG 11 compression to make the file size be <10 Mb (the personal Earthlink web limit is 10 Mb per mailbox). The low resolution image shown above, is about 1% the image size (10% x 10% dimensions) and is 416 Kb (Photoshop CS JPEG 5 of a reduced size image). 

 

 

Pathscan - microscope slide scanning

 

For additional Information on the PathScan system, see:

 

 

Meyer Instruments PathScan main page   

http://www.meyerinst.com/html/oem/pseiii/default.htm 

 

Meyer Instruments flyer

PathScan Enabler III Flyer in Adobe Acrobat (PDF) Format (File Size = 1.044 Mbytes)

 

Meyer Instruments Example Images

http://www.meyerinst.com/html/oem/pseiii/examples/default.htm (click on images on the Meyer page)

 

 

The Polaroid SprintScan 4000Plus has been discontinued (the original Polaroid Corp. went bankrupt), A new version of the PathScan Enabler, called the Pathscan III, because it holds 3 slides (!!!) works with the Microtek ArtixScan 4000tf. See Microtek's web site (Products -> Scanners -> Scientific) for:

 

ArtixScan 4000tf Path
4000-dpi film scanner to complement any lab or scientific workstation. Includes 1x3-inch slide holder, 35mm mounted slide holder, and 35mm filmstrip holder

 

The earliest paper I have found on using a 35 mm slide scanner to scan microscope slides is:

 

P.R. Montague, M. Meyer, R. Folberg 1995 Technique for the digital imaging of histopathologic preparations of eyes for research and publication. Ophthalmology 102: 1248-1251.

 

If you know of an earlier article on using a 35 mm slide scanner to scan microscope slides, please let me know (geomcnamara@earthlink.net).  

 

David Walker has several Micscape articles on using slide scanners to scan microscope slides:

 

D. Walker 1999 Topical Topics 3. An alternative use for A4 scanners. Micscapehttp://www.microscopy-uk.net/mag/indexmag.html?http://www.microscopy-uk.net/mag/artfeb99/toptips3.html

 

D. Walker 1999 Digital macroscopy in autumn with a flatbed scanner. Micscapehttp://www.microscopy-uk.org.uk/mag/artnov99/dwscan.html 

 

D. Walker 2004 Trials on scanning microscope slides of large subjects with a 35 mm Nikon Coolscan IV ED slide scanner. Micscape. http://www.microscopy-uk.net/mag/artaug04/dwslidescan.html 

 

David's 2004 article (March 2005) update added the following references from Paulette Herlin:

 

Nga Tran Kim, Nicolas Elie, Benoit Plancoulaine, Paulette Herlin, Michel Coster. An original approach for quantification of blood vessels on the whole tumour section. "Analytical Cellular Pathology" 25 (2003) 63-75.
Nicolas Elie, Benoit Plancoulaine, Jehan-Pierre Signolle, Paulette Herlin. A simple Way of Quantifying Immunostained Cell Nuclei on the whole histologic Section. "Cytometry" Part A 56A:37-45 (2003).
Nicolas Elie. Contribution à l’étude du stroma des tumeurs ovariennes humaines par traitement et analyse d’images numériques. Thèse de doctorat de l’Université de Caen Basse-Normandie, 16 décembre 2003.
Ronan Francoise, Jean Jacques Michels, Benoit Plancoulaine, Paulette Herlin. Optimal Resolution for automatic quantification of blood vessels on digitized images of the whole cancer section. "Image Analysis and Stereology" (2005) 24:1-9.
Nicolas Elie, Alexandre Labiche, Jean Jacques Michels, Paulette Herlin, Low resolution evaluation of ovarian tumor stromal compartment. Accepted for publication in "Image Analysis and Stereology", mars 2005.

 

Some other publications that use scanners to image microscope slides are:

 

C.M. Castro, Y. Yang, Z. Zhang, R.I. Linnoila (2000) Attenuation of pulmonary neuroendocrine differentiation in mice lacking Clara cell secretory protein. Lab Invest 80: 1533-1540. PMID: 11045570. 

Nikon LS-3510AF 35 mm film slide scanner (they used 9600 dpi scans, even though this is higher resolution than available at the time), MetaMorph image analysis - While at UIC (now MDC) I gave Ilona Linnoila and Tess Bunnag training on MetaMorph, circa 1996. 

 

UIC 1998 press release - Congratulations! National Cancer Institute wins Imaging Award Used MetaMorph to Boost Throughput, Quality. 

Dead UIC web link: pr-jun98-award.cfm - UIC is now MDC, a 7/30/2005 search for the press release web page was unsuccessful) I am posting a PDF of the webpage. 

"All of us here at Universal Imaging would like to congratulate Tess Bunnag and Ilona Linnoila of the National Cancer Institute for being selected as Imaging Solution of the Year by Advanced Imaging magazine. ... The magazine’s June 1998 Special Issue features profiles of individuals who merit special industry attention for their practical handling of digital imaging and image processing challenges. ... Tess and Ilona submitted their entry in the Scientific Visualization division, one of 10 categories broken out by the contest administrators."

 

I.A. Avramis, G. Christodoulopoulos, A. Suzuki, W.E. Laug, I. Gonzalez-Gomez, G. McNamara, E.A. Sausville, V.I. Avramis 2002 In vitro and in vivo evaluations of the tyrosine kinase inhibitor NSC 680410 against human leukemia and glioblastoma cell lines. Cancer Chemother Pharmacol 50: 479-489. PMID: 12451475. 

J. Qian, Z. Jiang, M. Li, P. Heaphy, Y.-H. Liu, G.M. Shackleford (2003) Mouse Wnt9b transforming activity, tissue-specific expression, and evolution. Genomics 81: 34–46. (CHLA Polaroid SprintScan 4000Plus and Meyer Instruments Pathscan adapter). 

I. Nordrum, M. Johansen, A. Amin, V. Isaksen, J.A. Ludvigsen (2004) Diagnostic accuracy of second-opinion diagnoses based on still images. Hum Pathol  35: 129-135. (Polaroid SprintScan 35 Film Scanner (maximum resolution, 2700 dpi; Polaroid Corp., Cambridge, MA) with a PathScan Enabler (Meyer Instrument, Houston, TX). 

T. Rother, C. Schrock-Pauli, C.S. Karmody, E. Bachor (2003) 3-D reconstruction of the vestibular endorgans in pediatric temporal bones. Hearing Res 185: 22-34. Nikon slide scanner, 4000 dpi. 

A. Gebert, K. Werner, W. Posselt (1998) Use of a digital film scanner to enhance low-power bright field photomicrography. Anat Embryol 198: 435-438. 

"A 35-mm film scanner NIKON LS-1000 (Nikon GmbH, Düsseldorf, Germany) was used for the experiments. As the scanner is designed for slide mounts, 50×50 mm in size, the microscopic glass slides, 76× 26mm in size, were fixed on a special slide holder made of brass (Fig. 1). ... Digital images were acquired using Silverfast software, version 3.1.4 (Lasersoft GmbH, Kiel, Germany) and processed using Photoshop software for Windows, version 4.0 (Adobe, Mountain View, Calif., USA). ...  To compare the digital scans with conventional photomicrographs, routine histological sections (n=120) served as test objects. These included sections of nervous tissue, embryos, parenchymal organs, gut wall, and larger vessels stained with H&E, Azan or Masson-Goldner trichrome staining."

D.A. Groneberg, C. Preiser (2002) Flatbed scanners as modern tools of digital reproduction in pathology. Histopathology 41: 171-172. (few hundred dollar flatbed scanner). 

J. Dahle, M. Kakar, H.B. Steen, O. Kaalhus (2004)  Automated counting of mammalian cell colonies by means of a flat bed scanner and image processing Cytometry 60A :182–188. 

 

The five articles below were references in Groneberg and Preiser:

L. Ventura (2002) Creating digital images of pathology specimens by using a flatbed scanner. Histopathology 40: 294.

K.T. Mai, W.A. Stinson, J. Swift, B.F. Burns, D.G. Perkins (2001)  Creating digital images of pathology specimens by using a flatbed scanner. Histopathology 39: 323–325. 

T.W. Beer (2000) Scanning of gross specimens. Am J Surg Pathol 24: 1170–1171.

B.F. Burns (1997) Creating low-power photomicrographs using a 35-mm digital slide scanner. Am J Surg Pathol  21:  865–866.

Azumi N. Creating low-power photomicrographs using a 35-mm digital slide scanner. Am J Surg Pathol 22: 908.

Ventura et al also had a 1999 article where they cite Montague et al (1995 - see above) as the first to use a 35 mm slide scanner for imaging histology slides.

L. Ventura, P. Leocata, P. Colimberti (1999) Digital scanning of histology sections. Am J Surg Pathol 23: 1435. 

They wrote, "In our department, we se an extremely simple method to scan histology sections. By using Gepe 24 x 36 mm slide mounts (BIWEX N.V., Holland), we put the tissue section directly on the glass center of the mount. This latter section is staied as required and covered with its glass counterpart, using synthetic resins as a mounting medium. Once dried, the slide is mounted into its plastic frame to be scanned as a conventional 35-mm color slide. ... The slide obtained, measuring 50x50 mm, does not require a handmade or commercial adapter and can be used in all digital film scannr models. It can also be stored to be used with common 35-mm slide projectors for teaching or presentation purposes. ... Slide mounts are a little bit more expensive than microscope slides, but they are used only in selected cases. Thus, the final cost is rather acceptable."

Another interesting use of flatbed scanners was to scan in mouse brains as well as TTC stained  tissue sections: 

E.J. Goldlust, R.P. Paczynski, Y.Y. He, C.Y. Hsu, M.P. Goldberg 1996 Automated measurement of infarct size with scanned images of triphenyltetrazolium chloride–stained rat brains. Stroke 27: 1657-1662. Free full text at http://stroke.ahajournals.org/cgi/content/full/27/9/1657 (TTC is 2,3,5-triphenyltetrazolium hydrochloride - th paper includes spectrophotometric data on the TTC dye absorption spectra). 

A 150x15-mm Petri dish was placed on the scanning surface of a flatbed color scanner (ScanJet IIc, Hewlett-Packard) and filled with approximately 100 mL of 10% formalin. Coronal sections (2 mm) from up to five brains were submerged in formalin. Care was taken to ensure that sections did not come into contact with each other and that the flat edge of tissue surfaces remained in contact with the bottom of the Petri dish. Each slice was placed with its largest surface toward the scanner (ie, sections from the anterior half of the brain were imaged with the posterior surface down, and sections from the posterior half were imaged with the anterior surface down; the middle section was not imaged). This procedure ensured that the area of each coronal section was counted once. ... The scanner was set to acquire 24-bit color images at 300 pixels per inch image resolution, with no color correction or image enhancement, and linear gain (gamma=1). The brightness setting (166) was set so that the background image was black (intensity=0). The contrast setting (182) was set so that the measured values did not exceed 255 for any color. The resulting image was saved as an uncompressed tagged image file format file and stored on magnetic or magneto-optical disk. ... When we used an optical test pattern (Edmund Scientific), the optical resolution of the scanner (at 400 pixels per inch, the highest setting) and that of the video camera (with 50-mm lens) were both approximately 200 µm. Scanner measurements of a 17x17-mm gray test specimen yielded uniform brightness values across the scanner surface. Scanned images of TTC-stained sections provided high spatial resolution and allowed observation of brain morphology. Color images demonstrated both infarcted areas and normal brain (Fig 3A). Infarct borders were less readily distinguished when the same brain sections were scanned with monochrome settings or when images were acquired with the monochrome camera. For quantitative image analysis, the color image was split into red, green, and blue component images. The red component image enhanced the distinction between gray and white matter, permitting inspection of brain morphology and anatomic landmarks (Fig 3B). The green component image provided markedly enhanced contrast between infarcted (bright) and uninfarcted (dark) brain regions (Fig 3C).

 

The following paper by Krout et al used a high end professional graphics scanner to scan (multiple) microscope slides:

K.E. Krout, J.M. Jenkins, A.D. Loewy (2002) High-resolution scanner for neuroanatomical analysis. Journal of Neuroscience Methods 113: 37-40. 

CreoScitex EverSmart Supreme scanner (CreoScitex Americas, Bedford, MA) connected to a Power Mac G3 (Apple Computer Inc., Cupertino, CA) was used to create the images. This scanner uses an 8000 element tri-linear CCD array on a 36 mm (1.417 in.) strip to produce an optical resolution of 5600 dpi. In addition, this CCD can be progressively moved along the length of the bed at 14 000 dpi using a precision stepper motor. Thus, when 14 000 dpi is used, pixels are interpolated along the width, but not the length, of the scanned image. Also, the CCD is automatically cooled to approximately 3 °C in order to reduce the level of noise. These features, along with on-the-fly image stitching, allow maximal resolution everywhere on the 305×432 mm bed. This scanner has two other features that significantly increase file size or scanning time, respectively, but these were not used for this report. First, the scanner is capable of producing 16-bit color images at full resolution. Second, a resampling algorithm called MaxDR, averages the data from up to four samples. This results in improved dynamic range, particularly in dark or shadow regions. However, this feature did not significantly improve the ability to identify neurons in the current application.

 

 

 

George McNamara

geomcnamara@earthlink.net 

 

 

George McNamara, Ph.D.

Division of Cancer Immunotherapeutics and Tumor Immunology

City of Hope National Medical Center

1500 E. Duarte Rd

Duarte, CA 91010

626-359-8111 ext 60035

gmcnamara@coh.org 

geomcnamara@earthlink.net 
http://home.earthlink.net/~geomcnamara        Personal web site (home page)

http://home.earthlink.net/~mpmicro                Personal web site (Multi-Probe Microscopy -- zip download)

http://home.earthlink.net/~pubspectra            Personal web site (fluorescence spectra downloads)

http://www.mcb.arizona.edu/IPC/fret/default.htm Fluorescent Spectra Web Server (Carl Boswell & GM)

 

Dr. McNamara is also a consultant for:

Congressman Julian Dixon Image Core
The Saban Research Institute of Childrens Hospital Los Angeles
4650 Sunset Blvd., MS 133, SRT 1016
Los Angeles, CA 90027

gmcnamara@chla.usc.edu

 

This page was last updated on 08/07/05.