Ignore:
Timestamp:
11/26/07 12:08:27 (13 years ago)
Author:
curtis
Message:

Add line breaks so that files are more readable when linked in the Trac.

Location:
trunk/loci/formats/doc
Files:
6 edited

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  • trunk/loci/formats/doc/gatan.html

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    22 
    3 <b>File format name:</b> Gatan Digital Micrograph 3<BR> 
    4 <b>Maintainer:</b> <a href="http://www.gatan.com">Gatan</a><BR> 
    5 <b>Software that produces this:</b>Gatan Digital Micrograph<BR> 
    6 <b>Other software that reads this format:</b>Gatan Digital Micrograph, <a href="http://rsb.info.nih.gov/ij/plugins/DM3_Reader.html">DM3_Reader ImageJ plugin</a>, <a href="http://blake.bcm.tmc.edu/eman/eman1">EMAN</a><BR> 
    7 <b>Specifications:</b> Nothing official; see <a href="http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html">here</a>.<BR> 
    8 <b>Structure:</b><BR> 
     3<b>File format name:</b> Gatan Digital Micrograph 3<br> 
     4<b>Maintainer:</b> <a href="http://www.gatan.com">Gatan</a><br> 
     5<b>Software that produces this:</b>Gatan Digital Micrograph<br> 
     6<b>Other software that reads this format:</b>Gatan Digital Micrograph, 
     7<a href="http://rsb.info.nih.gov/ij/plugins/DM3_Reader.html">DM3_Reader ImageJ 
     8plugin</a>, 
     9<a href="http://blake.bcm.tmc.edu/eman/eman1">EMAN</a><br> 
     10<b>Specifications:</b> Nothing official; see 
     11<a href="http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html">here</a>.<br> 
     12<b>Structure:</b><br> 
    913 
    10 See http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html<BR> 
    11 This format's structure is not always consistent, so there are probably some older or newer files that aren't opened properly.  Also, there is an older Gatan format - Digital Micrograph 2 - that is similar, but not supported.  If you have files in this format, please send them to us and we will add support. 
     14See http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html<br> 
     15This format's structure is not always consistent, so there are probably some 
     16older or newer files that aren't opened properly. Also, there is an older Gatan 
     17format, Digital Micrograph 2, that is similar, but not supported. If you have 
     18files in this format, please send them to us and we will add support. 
    1219 
    13 </html> 
     20</body></html> 
  • trunk/loci/formats/doc/ipw.html

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    22 
    3 <b>File format name:</b> Image-Pro Workspace<BR> 
    4 <b>Maintainer:</b> <a href="http://www.mediacy.com">Media Cybernetics</a><BR> 
    5 <b>Software that produces this:</b>Image-Pro Plus<BR> 
    6 <b>Other software that reads this format:</b>Image-Pro Plus<BR> 
    7 <b>Specifications:</b> none :-(<BR> 
    8 <b>Structure:</b><BR> 
     3<b>File format name:</b> Image-Pro Workspace<br> 
     4<b>Maintainer:</b> <a href="http://www.mediacy.com">Media Cybernetics</a><br> 
     5<b>Software that produces this:</b>Image-Pro Plus<br> 
     6<b>Other software that reads this format:</b>Image-Pro Plus<br> 
     7<b>Specifications:</b> none :-(<br> 
     8<b>Structure:</b><br> 
    99 
    10 IPW files are actually a variant of Microsoft's <a href="http://poi.apache.org/poifs/fileformat.html">OLE 2 document format</a>.  They contain embedded TIFF files, along with minimal metadata needed to read the images.  The IPW format does support storing multiple datasets within the same file; however, this is not implemented in Bio-Formats (if you have an IPW file with multiple datasets, please send it to us and we will add support for it).<BR><BR> 
    11 Note that you will need to install <a href="http://poi.apache.org">Jakarta POI</a> in order to read IPW files. 
     10IPW files are actually a variant of Microsoft's 
     11<a href="http://poi.apache.org/poifs/fileformat.html">OLE 2 document format</a>. 
     12They contain embedded TIFF files, along with minimal metadata needed to read 
     13the images. The IPW format does support storing multiple datasets within the 
     14same file; however, this is not implemented in Bio-Formats (if you have an IPW 
     15file with multiple datasets, please send it to us and we will add support for 
     16it).<br><br> 
    1217 
    13 </html> 
     18Note that you will need to install 
     19<a href="http://poi.apache.org">Jakarta POI</a> in order to read IPW files. 
     20 
     21</body></html> 
  • trunk/loci/formats/doc/nd2.html

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    22 
    33<p><b>File format name:</b> Nikon ND2 
    4 <p><b>Maintainer:</b><a href="http://www.nikonusa.com">Nikon</a> 
    5 <p><b>Software that produces these files:</b><a href="http://www.nis-elements.com">NIS Elements</a> 
    6 <p><b>Other software that reads this format:</b>NIS Elements<BR> 
    7 <p><b>Specifications:</b>none :-( 
    8 <p><b>Structure:</b><BR> 
     4<p><b>Maintainer:</b> <a href="http://www.nikonusa.com">Nikon</a> 
     5<p><b>Software that produces these files:</b> 
     6<a href="http://www.nis-elements.com">NIS Elements</a> 
     7<p><b>Other software that reads this format:</b> NIS Elements<br> 
     8<p><b>Specifications:</b> none :-( 
     9<p><b>Structure:</b><br> 
    910 
    10 ** All ND2 files are little-endian.<BR><BR> 
     11** All ND2 files are little-endian.<br><br> 
    1112 
    12 Old ND2:<BR><BR> 
     13Old ND2:<br><br> 
    1314 
    1415"Old" ND2 refers to files that were generated before May or June of 2007. 
    15 Basically, the file consists of a series of <a href="http://www.jpeg.org/jpeg2000/">JPEG-2000</a> codestreams, with a block of XML stuck on the end.<BR> 
     16Basically, the file consists of a series of 
     17<a href="http://www.jpeg.org/jpeg2000/">JPEG-2000</a> codestreams, 
     18with a block of XML stuck on the end.<br><br> 
    1619 
    17 <BR>'file' on an old ND2 file looks like this:<BR><BR> 
     20'file' on an old ND2 file looks like this:<br><br> 
    1821 
    19 user@machine:/data/$ file old_nd2.nd2<BR> 
    20 old_nd2.nd2: JPEG 2000 image data<BR> 
     22user@machine:/data/$ file old_nd2.nd2<br> 
     23old_nd2.nd2: JPEG 2000 image data<br> 
     24The first 8 bytes of the file should be: 0x00 00 00 0c 6a 50 20 20<br><br> 
    2125 
    22 The first 8 bytes of the file should be: 0x00 00 00 0c 6a 50 20 20<BR><BR> 
     26The only really noteworthy aspect of this format is that the XML block at the 
     27end of the file is malformed, so we have to parse it manually (meaning someone 
     28at some point may find missing or mislabeled metadata). 
    2329 
    24 The only really noteworthy aspect of this format is that the XML block at the end of the file is malformed, so we have to parse it manually (meaning someone at some point may find missing or mislabeled metadata). 
    25  
    26 <BR><BR>New ND2:<BR><BR> 
     30<br><br>New ND2:<br><br> 
    2731 
    2832"New" ND2 refers to files that were generated after May or June of 2007. 
    29 The new format is much preferred to the old format, in that the pixels are stored raw or zlib-compressed (and thus JAI is not required).<BR> 
     33The new format is much preferred to the old format, in that the pixels are 
     34stored raw or zlib-compressed (and thus JAI is not required).<br><br> 
    3035 
    31 <BR>'file' on a new ND2 file looks like this:<BR><BR> 
     36'file' on a new ND2 file looks like this:<br><br> 
    3237 
    33 user@machine:/data/$ file new_nd2.nd2<BR>  
    34 new_nd2.nd2: PARIX object not stripped<BR> 
     38user@machine:/data/$ file new_nd2.nd2<br> 
     39new_nd2.nd2: PARIX object not stripped<br> 
    3540 
    36 The file is divided into chunks of the following format:<BR> 
     41The file is divided into chunks of the following format:<br> 
     424 byte header - 0xda ce be 0a<br> 
     434 bytes - signed integer (length part 1)<br> 
     444 bytes - signed integer (length part 2)<br> 
     454 bytes - signed integer (ignored)<br> 
     46length pt 1 + length pt 2 bytes of data<br><br> 
    3747 
    38 4 byte header - 0xda ce be 0a<BR> 
    39 4 bytes - signed integer (length part 1)<BR> 
    40 4 bytes - signed integer (length part 2)<BR> 
    41 4 bytes - signed integer (ignored)<BR> 
    42 length pt 1 + length pt 2 bytes of data<BR><BR> 
     48The data portion of each chunk begins with a string identifer terminated by 
     49"!"; for pixel data, this is "ImageDataSeq|%n!", where %n is the plane number 
     50(indexed from 0). Otherwise, if the identifier begins with "Image%s!", you can 
     51expect a block of XML metadata. Unlike old ND2, this is valid XML, which we 
     52parse using SAX. 
     53<br><br> 
    4354 
    44 The data portion of each chunk begins with a string identifer terminated by "!"; for pixel data, this is "ImageDataSeq|%n!", where %n is the plane number (indexed from 0).  Otherwise, if the identifier begins with "Image%s!", you can expect a block of XML metadata.  Unlike old ND2, this is valid XML, which we parse using SAX. 
    45 <BR><BR> 
     55<p><b>Other notes:</b><ul> 
     56<li>JAI is required for reading old ND2 files</li> 
     57<li>We are aware that it takes too long to read image planes. This has always 
     58been the case, and will continue to be until JAI is improved or we implement a 
     59native JPEG2000 solution.</li> 
     60<li>The axis size detection logic is absolutely horrible, but it works.</li> 
     61<li>We were first made aware of "new" ND2 in June 2007 - the precise date it 
     62was released is unknown.</li> 
     63</ul> 
    4664 
    47 <p><b>Other notes:</b><BR> 
    48 - JAI is required for reading old ND2 files<BR> 
    49 - We are aware that it takes too long to read image planes.  This has always been the case, and will continue to be until JAI is improved or we implement a native JPEG2000 solution.<BR> 
    50 - The axis size detection logic is absolutely horrible, but it works.<BR> 
    51 - We were first made aware of "new" ND2 in June 2007 - the precise date it was released is unknown.<BR> 
    52  
    53 </html> 
     65</body></html> 
  • trunk/loci/formats/doc/perkin-elmer.html

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    22 
    3 <b>File format name:</b> Perkin-Elmer Ultraview<BR> 
    4 <b>Maintainer:</b> <a href="http://www.perkin-elmer.com">Perkin Elmer</a><BR> 
    5 <b>Software that produces this:</b><BR> 
    6 <b>Other software that reads this format:</b><BR> 
    7 <b>Specifications:</b> none :-(<BR> 
    8 <b>Structure:</b><BR> 
     3<b>File format name:</b> Perkin-Elmer Ultraview<br> 
     4<b>Maintainer:</b> <a href="http://www.perkin-elmer.com">Perkin Elmer</a><br> 
     5<b>Software that produces this:</b><br> 
     6<b>Other software that reads this format:</b><br> 
     7<b>Specifications:</b> none :-(<br> 
     8<b>Structure:</b><br> 
    99 
    10 Each dataset contains 4 or more metadata files with any of these extensions: .HTM, .csv, .tim, .zpo, .ano, .cfg, .rec, ...<BR> 
    11 Pixel data is stored separately (one plane per file), in TIFF format (.tif extension) or as raw data (variable length hexadecimal extension).  Raw data files have six magic bytes at the beginning of the file, which should be skipped. The metadata files do not indicate which format the pixels files are in - the directory must be manually searched.  <b>Thus, it is very important that all files in a Perkin-Elmer dataset are stored in the same directory.  Also, none of the files should be renamed, or else the entire dataset will likely be unreadable.</b><BR> 
    12 Metadata files are usually HTML, XML or plain-text (key/value pairs); the data they contain varies, but typically includes dimension information and basic instrumentation settings. 
     10Each dataset contains 4 or more metadata files with any of these extensions: 
     11.HTM, .csv, .tim, .zpo, .ano, .cfg, .rec, ...<br> 
     12Pixel data is stored separately (one plane per file), in TIFF format (.tif 
     13extension) or as raw data (variable length hexadecimal extension). Raw data 
     14files have six magic bytes at the beginning of the file, which should be 
     15skipped. The metadata files do not indicate which format the pixels files are 
     16in - the directory must be manually searched. 
     17<b>Thus, it is very important 
     18that all files in a Perkin-Elmer dataset are stored in the same directory. 
     19Also, none of the files should be renamed, or else the entire dataset will 
     20likely be unreadable.</b><br> 
     21Metadata files are usually HTML, XML or plain-text (key/value pairs); the data 
     22they contain varies, but typically includes dimension information and basic 
     23instrumentation settings. 
    1324 
    14 </html> 
     25</body></html> 
  • trunk/loci/formats/doc/seq.html

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    22 
    3 <b>File format name:</b> Image-Pro Sequence<BR> 
    4 <b>Maintainer:</b> <a href="http://www.mediacy.com">Media Cybernetics</a><BR> 
    5 <b>Software that produces this:</b>Image-Pro Plus<BR> 
    6 <b>Other software that reads this format:</b>Anything that supports TIFF<BR> 
    7 <b>Specifications:</b> none :-(<BR> 
    8 <b>Structure:</b><BR> 
     3<b>File format name:</b> Image-Pro Sequence<br> 
     4<b>Maintainer:</b> <a href="http://www.mediacy.com">Media Cybernetics</a><br> 
     5<b>Software that produces this:</b>Image-Pro Plus<br> 
     6<b>Other software that reads this format:</b>Anything that supports TIFF<br> 
     7<b>Specifications:</b> none :-(<br> 
     8<b>Structure:</b><br> 
    99 
    10 This is a TIFF variant with two extra tags - 50288 and 40105.  The purpose of 50288 is unknown; in all of our samples it is an array of 12 shorts, and the values are equal across all files (presumably it is some sort of format identifier).  The 40105 tag contains the frame rate.<BR><BR> 
     10This is a TIFF variant with two extra tags: 50288 and 40105. The purpose of 
     1150288 is unknown; in all of our samples it is an array of 12 shorts, and the 
     12values are equal across all files (presumably it is some sort of format 
     13identifier). The 40105 tag contains the frame rate.<br><br> 
    1114 
    12 In several of our samples, the TIFF comment contains the Z, C and T dimensions; however, this is not guaranteed to be the case. 
     15In several of our samples, the TIFF comment contains the Z, C and T dimensions; 
     16however, this is not guaranteed to be the case. 
    1317 
    14 </html> 
     18</body></html> 
  • trunk/loci/formats/doc/slidebook.html

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    22 
    3 <b>File format name:</b> Slidebook<BR> 
    4 <b>Maintainer:</b> <a href="http://www.intelligent-imaging.com">Intelligent Imaging</a>, <a href="http://www.olympus.com">Olympus</a><BR> 
    5 <b>Software that produces this:</b>Olympus/Intelligent Imaging Slidebook<BR> 
    6 <b>Other software that reads this format:</b>Olympus/Intelligent Imaging Slidebook<BR> 
    7 <b>Specifications:</b> none :-(<BR> 
    8 <b>Structure:</b><BR> 
     3<b>File format name:</b> Slidebook<br> 
     4<b>Maintainer:</b> 
     5<a href="http://www.intelligent-imaging.com">Intelligent Imaging</a>, 
     6<a href="http://www.olympus.com">Olympus</a><br> 
     7<b>Software that produces this:</b> Olympus/Intelligent Imaging Slidebook<br> 
     8<b>Other software that reads this format:</b> 
     9Olympus/Intelligent Imaging Slidebook<br> 
     10<b>Specifications:</b> none :-(<br> 
     11<b>Structure:</b><br> 
    912 
    10 <H3>Please note: we have not received any specifications or sample data from the manufacturers.  The structure described is based on a handful of files generated prior to June 2007.  If you have any information on this format, we would encourage you to contact us.</H3><BR><BR> 
     13<h3>Please note: we have not received any specifications or sample data from 
     14the manufacturers.  The structure described is based on a handful of files 
     15generated prior to June 2007.  If you have any information on this format, we 
     16would encourage you to contact us.</h3><br><br> 
    1117 
    1218Files appear to begin with 4 magic bytes - 0x6c 00 00 01 
    13 Following this is two bytes which indicate the endianness; if these bytes are both equal to 0x49 ('I'), then the data is little endian.  Otherwise, if these bytes are both equal to 0x4d ('M') then the data is big endian; any other value indicates an invalid file.<BR> 
    14 Analysis indicates that Slidebook files are made up of data blocks that are either 128 or 256 bytes in size.  Each block has a six byte identifier; the first byte is an ASCII character, and is used to determine what type of data is stored in the block.  The remaining five bytes can be ignored.<BR> 
     19Following this is two bytes which indicate the endianness; if these bytes are 
     20both equal to 0x49 ('I'), then the data is little endian.  Otherwise, if these 
     21bytes are both equal to 0x4d ('M') then the data is big endian; any other value 
     22indicates an invalid file.<br> 
     23Analysis indicates that Slidebook files are made up of data blocks that are 
     24either 128 or 256 bytes in size.  Each block has a six byte identifier; the 
     25first byte is an ASCII character, and is used to determine what type of data is 
     26stored in the block.  The remaining five bytes can be ignored.<br> 
    1527As far as we can tell, there are 3 types of data contained in Slidebook files: 
     28<ol> 
     29<li>generic, unreadable metadata</li> 
     30<li>pixel data</li> 
     31<li>annotations</li> 
     32</ol> 
     33Pixel data is found by looping through the file, skipping each data block until 
     34we find something that isn't identified as "generic metadata", and doesn't 
     35contain "Annotation".  It is important to do this through the entire file, 
     36because individual planes are stored contiguously, but we are not guaranteed 
     37to get all of the planes in one chunk.  All blocks of pixel data are 
     38immediately followed by a generic metadata block with the 'h' identifier 
     39byte.<br><br> 
    1640 
    17   (1) generic, unreadable metadata 
    18   (2) pixel data 
    19   (3) annotations 
     41The trickiest part of this format is trying to figure out the dimensions. 
     42We're pretty sure that the width and height are found in bytes 81-82 and 83-84 
     43(respectively) of an 'i' block.  The Z, C and T dimensions are calculated from 
     44the number of 'h', 'i' and 'u' blocks in the file.  These calculations are by 
     45no means guaranteed to be accurate.  We used to compute Z, C and T based on the 
     46count for each type of annotation; however, this proved to be even less 
     47accurate in some cases.  The chances of an inaccurate calculation are *greatly* 
     48increased if the Slidebook file contains image montage - we try to split 
     49montages into single images, but be warned that this may fail.<br><br> 
    2050 
    21 Pixel data is found by looping through the file, skipping each data block until we find something that isn't identified as "generic metadata", and doesn't contain "Annotation".  It is important to do this through the entire file, because individual planes are stored contiguously, but we are not guaranteed to get all of the planes in one chunk.  All blocks of pixel data are immediately followed by a generic metadata block with the 'h' identifier byte.<BR><BR> 
     51Finally, as far as we know, all Slidebook files use 16 bits per pixel.<br><br> 
    2252 
    23 The trickiest part of this format is trying to figure out the dimensions.  We're pretty sure that the width and height are found in bytes 81-82 and 83-84 (respectively) of an 'i' block.  The Z, C and T dimensions are calculated from the number of 'h', 'i' and 'u' blocks in the file.  These calculations are by no means guaranteed to be accurate.  We used to compute Z, C and T based on the count for each type of annotation; however, this proved to be even less accurate in some cases.  The chances of an inaccurate calculation are *greatly* increased if the Slidebook file contains image montage - we try to split montages into single images, but be warned that this may fail.<BR><BR> 
    24 Finally, as far as we know, all Slidebook files use 16 bits per pixel.<BR><BR> 
    25  
    26 </html> 
     53</body></html> 
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