Following transfer, the gzipped tar files must be unzipped by gunzip or winzip and de-tarred with tar xvf filename.tar in the directory that you want.
The packaged, compressed files come with the file extension ".tar.gz" and can be unzipped using WinZip or similar. WinZip will detect a single file and prompt you for the file's extension, which is ".tar". It will then proceed to extract the individual files.
Alternatively, if you prefer to use tar for DOS, you can download tar.exe and other handy programs for emulating unix in a DOS window:
ftp.ualg.pt login anonymous;
password your email address
All images were acquired using brightfield light microscopy and a 1018x1008 pixel CCD camera. All images are 8-bit greyscales. The image acquisition protocol is still under development, with image quality still improving slightly; hence, earlier batches are not necessarily of the same standard as later ones. The image format is TIFF and file sizes range from approximately 100 K to 1 Mbyte, the majority being between 200 and 500 KB. Below you find a list of what the files contain and their sizes.
Most of the images show single diatom valves only (the exception is "views.zip" which shows lower magnification views as are typical of strewn diatom slides). All images are unprocessed at this stage; no contrast adjustments have been made or contaminating structures removed. As a result, most images look "flat", i.e. lack contrast. This is a consequence of the acquisition protocol, in which we have maximised resolution at the cost of contrast at the time of capture. Users will have to carry out any adjustments themselves (like a histogram equalisation for visualisation purposes).
Earlier files are labelled with six-digit numbers; those followed by a "b", indicate that a scale bar has been added. From file 00435 onwards, the filename consists of a six-digit number (unique to each individual diatom being photographed) followed by two letters that are interpretable only by reference to the index file. To fully represent the valve morphologically, more than one image are now captured per valve, with each image showing a different focal plane. The first letter after the number in the file name indicates the focal plane at which the image was taken, while the second indicates different versions of the image (whether or not preprocessed/edited, and whether or not a scale bar is present). The index file located in the directory lists the file numbers and details respective taxon names, pixel widths, image types etc. It is provided both as a rich text format file and an Excel spreadsheet ("index.rtf" and "index.xls" respectively). Each image is also represented by a version containing scale bars, and additonally, pixel width information is given for each image in the index file.
Taxon names for each image are provided in the index file. Names used here are largely as in the DIATCODE checklist of British Diatoms (available at http://www.geog.ucl.ac.uk/~pmalipha/checklis.htm), with some additional recent taxonomic changes included. In some cases, like the genus Achnanthes, we are aware that classificatory changes are under way but until their completion the existing taxonomy will be used.
A list of the literature used for identification is provided below, and the index file indicates the source used for the identification for each specimen. Identifications were carried out by M. Bayer, A. Clarke, R. Head and M. Lewis.
Please note that this is work in progress and mistakes do occur due to the volume of data. We appreciate users' feedback both on imaging and taxonomic issues, so please feel free to get in touch with us (contact: firstname.lastname@example.org).
EVERYBODY IS FREE TO USE THE IMAGES PROVIDED, BUT
1. ANY USE OF THE IMAGES FOR COMMERCIAL PURPOSES IS PROHIBITED, AND
2. ANY DOCUMENT, PRINTED OR ELECTRONIC, CONTAINING IMAGE MATERIAL IN ORIGINAL OR PROCESSED FORM MUST REFER TO AND ACKNOWLEDGE THE ADIAC PROJECT. ****************************************************************************************
The public account contains approx. 3,400 images packaged in manageable batch files.
Contents of files:
index.rtf: file inventory as rich text, complete with taxon names and pixel widths
index.xls: same file as Excel 5.0 spreadsheet
batch1.tar.gz: images 000058b to 000250b, normal images with scale bars, 30 mb
batch2.tar.gz: images 000251b to 000388b, normal images, with scale bars, 20 mb
batch3.tar.gz: images 000435 to 000495, multiple focal planes, 25 mb
batch4.tar.gz: images 000496 to 000544, multiple focal planes, 26 mb
batch5.tar.gz: images 000545 to 000608, multiple focal planes, 25 mb
batch6.tar.gz: images 000609 to 000660, multiple focal planes, 26 mb
batch7.tar.gz: images 000661 to 000717, multiple focal planes, 30 mb
batch8.tar.gz: images 000718 to 000740, multiple focal planes, 14 mb
batch9.tar.gz: images 000741 to 000768, multiple focal planes, 14 mb
batch10.tar.gz: images 000769 to 000835, multiple focal planes, 33 mb
batch11.tar.gz: images 000836 to 000902, multiple focal planes, 31 mb
batch12.tar.gz,images 000718 to 000740, several focal planes per specimen,14 mb
batch13.tar.gz,images 000741 to 000768, several focal planes per specimen,14 mb
batch14.tar.gz,images 000769 to 000835, several focal planes per specimen,32 mb
batch15.tar.gz,images 000836 to 000902, several focal planes per specimen,34 mb
batch16.tar.gz,images 000903 to 000960, several focal planes per specimen,10 mb
batch17.tar.gz,images 001171 to 001277, several focal planes per specimen,19 mb
batch18.tar.gz,images 001278 to 001560, one focal plane per specimen, 260 files,47 mb
batch19.tar.gz,images 001561 to 001885, one focal plane per specimen, 325 files,32 mb
batch20.tar.gz,images 001886 to 002023, one focal plane per specimen, 138 files,26 mb
batch21.tar.gz,images 002024 to 002225, one focal plane per specimen, 202 files,42 mb
views.tar.gz: images 000389 to 000408, test images (multiple valves) 14 mb
index.txt and index.xls: lists with taxon names and other image info pertaining to images in above batches, as text and Excel 97 files, respectively
Literature used for identification of specimens:
Chang, T.-P. & Steinberg, C. (1988): Epiphytische Diatomeen auf Cymatopleura und Nitzschia. Diatom Research 3: 203-216.
Cox, E.J. (1987): Placoneis Mereschkowsky: The reevaluation of a diatom genus originally characterized by its chloroplast type. Diatom Research 2: 145-157.
Flower, R.J. , Jones, V.J. & Round, F.E. (1996): The distribution and classification of the problematic Fragilaria (virescens v.) exigua Grun./Fragilaria exiguiformis (Grun.) Lange-Bertalot: a new species or a new genus? Diatom Research 11: 41-57.
Hartley, B. (1996): An Atlas of British Diatoms. Biopress Limited, Bristol, UK. 601 pp.
Hasle, G.R. & Syvertsen, E.E. (1996): Marine Diatoms. Pp. 5- 386 in "Identifying Marine Diatoms and Dinoflagellates", edited by Tomas, C.R. Academic Press, London, UK.
Hendey, N.I. (1964): An Introductory Account of the Smaller Algae of British Coastal Waters. Part V Bacillariophyceae (Diatoms). H.M. Stationery Office. 317 pp.
Hustedt, F. (1930): Die Kieselalgen. Part 1. Reprinted 1962, Verlag von J. Cramer, Weinheim, Germany. 920 pp.
Kociolek, J.P. & Stoermer, E.F. (1987): Ultrastructure of Cymbella sinuata and its allies (Bacillariophyceae), and their transfer to Reimeria, gen. nov. Syst. Bot. 12: 451-459.
Krammer, K. & Lange-Bertalot, H. 1986-1991. Bacillariophyceae, Parts 1-4. Volume 2 of "Süsswasserflora von Mitteleuropa", edited by Ettl, H. et al. Gustav Fischer Verlag, Stuttgart, Germany.
Krammer, K. (1992): Pinnularia - eine Monographie der europäischen Taxa. Bibliotheca Diatomologica Vol. 26. Verlag J. Cramer, Berlin, Germany. 353 pp.
Krammer, K. (1997): Die cymbelloiden Diatomeen. Bibliotheca Diatomologica Vol. 37. Verlag J. Cramer, Berlin, Germany. 469 pp.
Lange-Bertalot, H. & Metzeltin, D. 1996. Indicators of Oligotrophy. Iconographia Diatomologica Vol. 2. Koeltz Scientific Books, Königstein, Germany. 390 pp.
Mann, D.G. & Droop, S.J.M. (1996): Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 336: 19-32.
Mann, D.G. (1989a). The species concept in diatoms: evidence for morphologically distinct sympatric gamodemes in four epipelic species. Plant Systematics and Evolution, 164, 215-237.
Ricard, M. (1987): Diatomophycées. Atlas du phytoplancton marin, vol 2: 1-297, Paris.
Round, F.E., Crawford, R.M. & Mann, D.G. (1990): The diatoms. Biology & morphology of the genera. Cambridge Univ. Press. 1- 747.
Simonsen, R. (1987): Atlas and Catalogue of the diatom types of Friedrich Hustedt. Vol. 1: Catalogue. pp. 1-525. Vol. 2: Atlas, Taf. 1-395. Vol. 3: Atlas, Taf. 396-772. J. Cramer Berlin/Stuttgart.
Snoeijs, P. & Potapova, M. (1995): Intercalibration and distribution of diatom species in the Baltic Sea. Volume 3. Opulus Press, Uppsala. 125 pp.
Snoeijs, P. & Vilbaste (1994): Intercalibration and distribution of diatom species in the Baltic Sea. Volume 2. Opulus Press, Uppsala. 125 pp.
Snoeijs, P. (1992): Studies in the Tabularia fasciculata complex. Diatom Research 7: 313-344.
Snoeijs, P. (1993): Intercalibration and distribution of diatom species in the Baltic Sea. Volume 1. Opulus Press, Uppsala. 130 pp.
Van der Werff, A. & Huls, H. 1976. Diatomeenflora van Nederland. Otto Koeltz Science Publishers, Königstein, Germany.
Williams, D.M. & Round, F.E. (1987): Revision of the genus Fragilaria. Diatom Research 2: 267-288.
Witkowski, A. (1994): Recent and fossil diatom flora of the Gulf
of Gdansk, Southern Baltic Sea. Bibliotheca Diatomologica Vol. 28.
Verlag J. Cramer, Berlin, Germany. 313 pp.
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