United States (EN)
Select your region or country.
NDP.image File Format
The NDPi format is the native format of the Hamamatsu NanoZoomer digital slide scanner and is based on the TIFF 6.0 international standard. Readers not already familiar with TIFF 6.0 should refer to the TIFF 6.0 specification in conjunction with this document. TIFF was chosen because it is a widely recognized standard format that is flexible enough to support virtual microscopy applications.
Source: ITU（International Telecommunication Union）
Image Structure and Viewing Performance
TIFF supports a variety of compression formats. Image data within an NDPi image can be compressed using JPEG. When JPEG is used, it is stored according to Technical Note 2 of the TIFF 6.0 specification as complete JFIF streams. An NDPi image contains several sub-images stored in a multi-page TIFF format (Figure 1).
To maximize the speed of decoding a region of interest, NDPi images typically contain multiple copies of the same image at lower resolutions, in addition to the source resolution image.
These images have lens magnification (tag: 65421 described below) calculated from the resolution and the source lens magnification at the time the original image was scanned.
This layered structure is referred to as a pyramid, where images of decreasing size are stacked to form a pyramid shape. There are no restrictions on the number of pyramid levels or the ratio between them. An NDPi reader simply selects the lowest resolution image that meets or exceeds the required resolution for the requested region.
Figure 1︓Structure of an NDPi Image
Advanced Image Data Support
NDPi images support multi-plane storage, meaning images can be captured at different focus (Z) positions (tag: 65424).
Each focal plane image also includes pyramid levels as described above.
Additional related images, such as overview images of the entire slide including labels, can optionally be stored within the file (described at tag: 65421).
TIFF supports both little endian (Intel) and big endian (Motorola) byte orders, but NDPi images are always stored using little endian.
Indexing for Fast Data Access
JPEG is a variable-length stream format, which means decoding even a small region can require parsing the entire stream. To reduce this overhead, NDPi images
include indexes that allow readers to skip directly to positions near the required data. Each MCU (minimum coding unit) in JPEG normally depends on the
previous MCU. NDPi avoids this requirement by using JPEG restart markers. These markers appear at fixed intervals and reset the encoder state, eliminating
dependencies between segments and aligning the bitstream to byte boundaries. Large NDPi images typically include an index that points to the position of each
restart marker. The interval between restart markers can be determined from the JFIF header. Smaller images may omit indexes and restart markers when they
provide little benefit.
Standard Metadata (TIFF Tags)
The size, resolution, and other properties of each sub-image are defined using standard TIFF tags, including:
Standard Tags
| Item | Tag | Type | Description |
|---|---|---|---|
| Image Width | 256 | SHORT / LONG | The number of columns in the image |
| Image Height | 257 | SHORT / LONG | The number of rows in the image |
| Make | 271 | ASCII | Manufacturer of the scanner (e.g. "Hamamatsu") |
| Model | 272 | ASCII | Scanner model number (e.g. "C13220-01MD") |
| X Resolution | 282 | RATIONAL | Pixels per resolution unit (width direction) |
| Y Resolution | 283 | RATIONAL | Pixels per resolution unit (height direction) |
| Resolution Unit | 296 | SHORT | Measurement unit (centimeter) |
| Software | 305 | ASCII | Software name and version |
| Date Time | 306 | ASCII | Image creation date and time |
Extended Metadata (Private Tags)
Information not supported by standard TIFF tags is managed using private tags that provide detailed, NDPi-specific information.
Basic Information
| Item | Tag | Type | Description |
|---|---|---|---|
| Version | 65420 | LONG | NDPI version (currently 1) |
| Reference | 65427 | ASCII | Slide reference |
Image / Magnification
| Item | Tag | Type | Description |
|---|---|---|---|
| Lens/Image Type | 65421 | FLOAT | Lens equivalent magnification (relative value) |
※Notes
- -1: Overview image
- -2: Tissue map
Position & Focus
| Item | Tag | Type | Description |
|---|---|---|---|
| Physical X | 65422 | SLONG | Center position (nm) |
| Physical Y | 65423 | SLONG | Center position (nm) |
| Physical Z | 65424 | SLONG | Focus position (nm) |
| Focus Points | 65439 | SLONG (array) | Focus points (X, Y, Z) |
| Focus Point Regions | 65440 | SLONG | Mapping of focus points and regions |
Image Acquisition
| Item | Tag | Type | Description |
|---|---|---|---|
| Capture Mode | 65441 | SLONG | Imaging mode |
| Exposure Ratio | 65435 | SLONG | Exposure multiplier |
| Gain Multipliers | 65436–65438 | SLONG | Channel gain |
| Exposure Time | 65454 | LONG | Exposure time |
| Wavelength | 65451 | FLOAT | Emission wavelength |
Device / Scan Information
| Item | Tag | Type | Description |
|---|---|---|---|
| Hardware Serial Number | 65442 | ASCII | Scanner serial number |
| Firmware Version | 65448 | ASCII | Firmware version |
| Calibration Info | 65449 | ASCII | Calibration data |
| Scan Time | 65456 | LONG | Scan duration |
| Focus Time | 65455 | LONG | Focus duration |
| Write Time | 65457 | LONG | File writing time |
| Refocus Interval | 65445 | SLONG | Refocus interval |
| Focus Offset | 65446 | SLONG | Focus offset |
| Fully Automatic Focus | 65458 | LONG | Fully automatic focus flag |
Compression / Data Structure
| Item | Tag | Type | Description |
|---|---|---|---|
| JPEG Quality | 65444 | SLONG | Compression quality |
| Restart Marker Index | 65426 | LONG (array) | Restart marker offsets |
| Restart Marker Index High | 65432 | LONG (array) | High-order offsets (for >4GB files) |
Additional Information
| Item | Tag | Type | Description |
|---|---|---|---|
| Label Obscured | 65450 | LONG | Label masking flag |
| Lamp Age | 65453 | LONG | Lamp usage time |
Identification / Regulation
| Item | Tag | Type | Description |
|---|---|---|---|
| Barcodes | 65468–65475 | ASCII | Up to 8 barcode regions |
| Medical Regulation | 65476 | ASCII | Regulation (RUO / IVR / USA) |
Deviations from the TIFF Specification
TIFF is a highly versatile format that supports private tags, enabling NDPi images to include additional necessary information while remaining compliant with standard TIFF specifications. However, because NanoZoomer produces extremely large images, extensions beyond the original TIFF/JFIF standards were introduced.
JPEG Images Larger Than 64k Pixels
The JFIF header in a JPEG stream allocates only 16 bits for each image dimension, limiting sizes to 65,536 pixels. NanoZoomer images often exceed this limit.
When JPEG images are stored within a TIFF file (see TIFF Tech Note 2), dimensions are recorded in two places: the TIFF IFD entries and the JFIF header.
Normally, these values match; however, if an image exceeds the JFIF 16-bit limit, its header values are set to zero. The TIFF IFD entries use 32-bit values and
will always contain the correct width and height.
NDPi Files Greater than 4 GB
TIFF uses file offsets to locate data within the file. Since these offsets are stored as 32-bit unsigned integers, the format is limited to a maximum file size of 4
GB. While many NanoZoomer images fall within this limit, some, particularly those utilizing multi-level scanning, can exceed it. In such cases, the format is
extended as follows:
- Directly after the TIFF File Header, an additional DWORD is included to represent the high-order portion of the file offset pointing to the first IFD (Image File Directory).
- Immediately after each IFD, there is a DWORD that specifies the high-order part of the file offset to the next IFD.
- Following this additional DWORD, a series of DWORDs, equal in number to the entries in the IFD, are provided. These represent the high-order parts of the offsets for corresponding IFD entries. For entries that contain actual data (rather than offsets), these values will be zero and should be ignored.
The benefit of this approach is that files under 4 GB remain compliant with the standard TIFF format. These extensions are only used when necessary (i.e. when
a file exceeds the 4 GB limit). The creator does not need to predict whether an image will exceed this threshold; it can simply write zeros in the extra fields,
knowing they will be ignored by standard readers. A reader should only check for these additional features if the file size is greater than 4 GB. For smaller files,
their presence should not be assumed, and an NDPi file under 4 GB without these extensions is still valid.
Short Strings
Standard TIFF stores strings consisting of three characters or less directly within the IFD. NDPi files always store strings outside of the IFD even if they are short
enough to fit inside it.
* Specifications is subject to change without notice.
- Confirmation
-
It looks like you're in the . If this is not your location, please select the correct region or country below.
You're headed to Hamamatsu Photonics website for US (English). If you want to view an other country's site, the optimized information will be provided by selecting options below.
In order to use this website comfortably, we use cookies. For cookie details please see our cookie policy.
- Cookie Policy
-
This website or its third-party tools use cookies, which are necessary to its functioning and required to achieve the purposes illustrated in this cookie policy. By closing the cookie warning banner, scrolling the page, clicking a link or continuing to browse otherwise, you agree to the use of cookies.
Hamamatsu uses cookies in order to enhance your experience on our website and ensure that our website functions.
You can visit this page at any time to learn more about cookies, get the most up to date information on how we use cookies and manage your cookie settings. We will not use cookies for any purpose other than the ones stated, but please note that we reserve the right to update our cookies.
1. What are cookies?
For modern websites to work according to visitor’s expectations, they need to collect certain basic information about visitors. To do this, a site will create small text files which are placed on visitor’s devices (computer or mobile) - these files are known as cookies when you access a website. Cookies are used in order to make websites function and work efficiently. Cookies are uniquely assigned to each visitor and can only be read by a web server in the domain that issued the cookie to the visitor. Cookies cannot be used to run programs or deliver viruses to a visitor’s device.
Cookies do various jobs which make the visitor’s experience of the internet much smoother and more interactive. For instance, cookies are used to remember the visitor’s preferences on sites they visit often, to remember language preference and to help navigate between pages more efficiently. Much, though not all, of the data collected is anonymous, though some of it is designed to detect browsing patterns and approximate geographical location to improve the visitor experience.
Certain type of cookies may require the data subject’s consent before storing them on the computer.
2. What are the different types of cookies?
This website uses two types of cookies:
- First party cookies. For our website, the first party cookies are controlled and maintained by Hamamatsu. No other parties have access to these cookies.
- Third party cookies. These cookies are implemented by organizations outside Hamamatsu. We do not have access to the data in these cookies, but we use these cookies to improve the overall website experience.
3. How do we use cookies?
This website uses cookies for following purposes:
- Certain cookies are necessary for our website to function. These are strictly necessary cookies and are required to enable website access, support navigation or provide relevant content. These cookies direct you to the correct region or country, and support security and ecommerce. Strictly necessary cookies also enforce your privacy preferences. Without these strictly necessary cookies, much of our website will not function.
- Analytics cookies are used to track website usage. This data enables us to improve our website usability, performance and website administration. In our analytics cookies, we do not store any personal identifying information.
- Functionality cookies. These are used to recognize you when you return to our website. This enables us to personalize our content for you, greet you by name and remember your preferences (for example, your choice of language or region).
- These cookies record your visit to our website, the pages you have visited and the links you have followed. We will use this information to make our website and the advertising displayed on it more relevant to your interests. We may also share this information with third parties for this purpose.
Cookies help us help you. Through the use of cookies, we learn what is important to our visitors and we develop and enhance website content and functionality to support your experience. Much of our website can be accessed if cookies are disabled, however certain website functions may not work. And, we believe your current and future visits will be enhanced if cookies are enabled.
4. Which cookies do we use?
There are two ways to manage cookie preferences.
- You can set your cookie preferences on your device or in your browser.
- You can set your cookie preferences at the website level.
If you don’t want to receive cookies, you can modify your browser so that it notifies you when cookies are sent to it or you can refuse cookies altogether. You can also delete cookies that have already been set.
If you wish to restrict or block web browser cookies which are set on your device then you can do this through your browser settings; the Help function within your browser should tell you how. Alternatively, you may wish to visit www.aboutcookies.org, which contains comprehensive information on how to do this on a wide variety of desktop browsers.
5. What are Internet tags and how do we use them with cookies?
Occasionally, we may use internet tags (also known as action tags, single-pixel GIFs, clear GIFs, invisible GIFs and 1-by-1 GIFs) at this site and may deploy these tags/cookies through a third-party advertising partner or a web analytical service partner which may be located and store the respective information (including your IP-address) in a foreign country. These tags/cookies are placed on both online advertisements that bring users to this site and on different pages of this site. We use this technology to measure the visitors' responses to our sites and the effectiveness of our advertising campaigns (including how many times a page is opened and which information is consulted) as well as to evaluate your use of this website. The third-party partner or the web analytical service partner may be able to collect data about visitors to our and other sites because of these internet tags/cookies, may compose reports regarding the website’s activity for us and may provide further services which are related to the use of the website and the internet. They may provide such information to other parties if there is a legal requirement that they do so, or if they hire the other parties to process information on their behalf.
If you would like more information about web tags and cookies associated with on-line advertising or to opt-out of third-party collection of this information, please visit the Network Advertising Initiative website http://www.networkadvertising.org.
6. Analytics and Advertisement Cookies
We use third-party cookies (such as Google Analytics) to track visitors on our website, to get reports about how visitors use the website and to inform, optimize and serve ads based on someone's past visits to our website.
You may opt-out of Google Analytics cookies by the websites provided by Google:
https://tools.google.com/dlpage/gaoptout?hl=en
As provided in this Privacy Policy (Article 5), you can learn more about opt-out cookies by the website provided by Network Advertising Initiative:
http://www.networkadvertising.org
We inform you that in such case you will not be able to wholly use all functions of our website.
Close