Kamis, 15 Januari 2009

MODIS phytoplankton-ENVI

MODIS phytoplankton-ENVI

I would like to discuss about "MODIS phytoplankton-ENVI".
title of this my blog post today is about Aqua/Terra MODIS image processing for detecting phytoplankton using software ENVI.

Let's start this discussion from the last word :"ENVI"

What is ENVI??

We know that ENVI is great image processing and analyzing geospatial imagery.
ENVI is the premier software solution for processing and analyzing geospatial imagery used by GIS professionals, scientists, researchers, and image analysts around the world. ENVI software combines the latest spectral image processing and image analysis technology with an intuitive, user-friendly interface to help you get meaningful information from imagery.

ENVI provides us MODIS Toolkit and Ocean Color Plug-ins (previous posting : http://ajiputrap.blogspot.com/2008/12/modis-toolkit-and-ocean-color-plug-ins.html)
ENVI help us in MODIS image processing with geometric correction (bow-tie correction).

- I have uploaded in my esnips simple tutorial Aqua/Terra MODIS image processing using ENVI 4.x


download this tutorial:
pengolahan citra modis dengan envi.pdf
-- step by step from open MODIS HDF (Level 1B), MODIS Geometric Correction (include Bow-Tie Correction), Radiometric Correction for Reflectance and Radiance Bands (use Band Math).
Another tutorial files can be downloaded in http://www.esnips.com/web/perdana09-article :
- SeaDAS_4_AquaMODIS.pdf
Tutorial Aqua/Terra MODIS image processing using SeaDAS software
- Langkah Order Citra MODIS.pdf
How to order MODIS (level 1B at Ladsweb)

2. phytoplankton
phytoplankton ??
Phytoplankton are the autotrophic component of the plankton community. The name comes from the Greek words phyton, or "plant", and πλαγκτος ("planktos"), meaning "wanderer" or "drifter".[1] Most phytoplankton are too small to be individually seen with the unaided eye. However, when present in high enough numbers, they may appear as a green discoloration of the water due to the presence of chlorophyll within their cells (although the actual color may vary with the species of phytoplankton present due to varying levels of chlorophyll or the presence of accessory pigments such as phycobiliproteins, xanthophylls, etc.).

Phytoplankton obtain energy through a process called photosynthesis and must therefore live in the well-lit surface layer (termed the euphotic zone) of an ocean, sea, lake, or other body of water.

Phytoplankton are a key food item in both aquaculture and mariculture. Both utilize phytoplankton for the feeding of the animals being farmed. In mariculture, the phytoplankton is naturally occurring and is introduced into enclosures with the normal circulation of seawater. In aquaculture, phytoplankton must be obtained and introduced directly.


1. ^ Thurman, H. V. (1997). Introductory Oceanography. New Jersey, USA: Prentice Hall College. ISBN 0132620723.
2. ^ "Satellite Sees Ocean Plants Increase, Coasts Greening". NASA (2 March 2005). Retrieved on 12 January 2009.
3. ^ Richtel, M. (May 1, 2007), "Recruiting Plankton to Fight Global Warming", New York Times, http://www.nytimes.com/2007/05/01/business/01plankton.html?ref=science
4. ^ Hallegraeff, G.M. (2003). Harmful algal blooms: a global overview. in Hallegraeff, G.M., Andewrson, D.M. and Cembella, A.D. (eds) 2003. Manual on Harmful Marine Microalgae. UNESCO, Paris
5. ^ G.E. Hutchinson (1961). "The paradox of the plankton". Am. Nat. 95: 137–145. doi:10.1086/282171.
6. ^ a b c d McVey, James P., Nai-Hsien Chao, and Cheng-Sheng Lee. CRC Handbook of Mariculture Vol. 1 : Crustacean Aquaculture. New York: C R C P LLC, 1993.

== source information : http://en.wikipedia.org/wiki/Phytoplankton ==

interesting question about phyto...

Where Are Phytoplankton?

The distribution of phytoplankton in the ocean have been measured by special instruments in space since 1979. The instruments, called ocean-color scanners, measure the color of the ocean. Color is proportional to the amount of chlorophyll pigments close to the surface, except in sediment-rich water very close to coasts. And the amount of chlorophyll is proportional to the amount of phytoplankton in the water. Water with great numbers of phytoplankton are green. Pure ocean water is deep navy blue.

The first ocean-color scanner, the Coastal Zone Color Scanner, was launched on the Nimbus-7 satellite in 1978. It was followed many years later by SeaWiFS (Sea-viewing Wide Field-of-view Sensor) on the Seastar satellite launched in 1997. The most recent color scanner is MODIS (Moderate Resolution Imaging Spectrometer) on the Terra spacecraft launched in 1999 and the Aqua satellite launched in 2002.

more information about distribution of phyto...read this article : Distribution of Plankton

summary from the article
Phytoplankton are abundant in regions where:
1. Winds are able to mix nutrients up into near surface waters from deeper in the ocean, or
2. Where Ekman transports driven by the winds pulls water up from deeper in the ocean,
a. When winds blow toward the equator along west coasts of continents, and
b. When the average winds blowing at different speeds and directions cause divergence of the Ekman transports,provided a small amount iron needed by the protists is in the water.

--- MODIS (Moderate Resolution Imaging Spectrometer) on the Terra spacecraft and the Aqua satellite help us daily in monitoring or detecting phytoplankton. ---

3. MODIS (Moderate Resolution Imaging Spectrometer)
please read previously article about MODIS (http://ajiputrap.blogspot.com/search/label/MODIS)
or directly from http://modis.gsfc.nasa.gov

Step by step Aqua/Terra MODIS (Level 1B) image processing using ENVI 4.2 software:
1. Download MODIS data level 1B 1km resolution from ladsweb...
2. Open HDF MODIS in ENVI 4.x
File -> Open External File -> Generic Format -> HDF (http://ajiputrap.blogspot.com/2008/12/modis-hdf-hierarchical-data-format.html or http://ajiputrap.blogspot.com/search/label/HDF)
3. Geometric Correction, include Bow-Tie Correction*
Bowtie Correction aims to improve image at overlapped data. Overlap occurs because there is increasing instantaneous field of view (IFOV) of 1x1 km in the lowest point (nadir). Being close to almost 2 x 5 km at the maximum scan angle is 55 degree.
After MODIS DATA geometrically corrected, then go to the next step
4. Radiometric Correction
Radiometric Correction in ENVI use Band Math (ENVI main menu, choose Basic Tool -> Band Math)

Reflectance Bands calculated for visible and thermal infrared (1 – 19 and 26 bands) with this formula:
Refb = Ref_Scaleb * (Bb - Ref_offsetsb)

where: Refb = Reflectance of band- b
Ref_Scaleb = Reflectance scale
Bb = Band -b
Ref_offsetsb = Reflectance offset band- b

-- information about reflectance scale and offset we may get it from HDF Dataset (http://ajiputrap.blogspot.com/2008/12/modis-hdf-hierarchical-data-format.html or http://ajiputrap.blogspot.com/search/label/HDF)

5. Chlorophyll-a algorithm with Band Math
After we get geometric and radiometrically corrected MODIS image, we continue to the main step : detecting Chlorophyll-a

Fitoplankton that is on a layer of light contains Chlorophyll-a useful for photosynthesis. Chlorophyll-a able to absorb a light blue and green, so it can detect the existence fitoplankton based on the ability of these Chlorophyll-a.

MODIS can help us to detecting Chlorophyll-a (Chlor-a) with formula or algorithm from Carder et al. :


where : B10 = Reflecance of Band 10
B12 = Reflecance of Band 12
- above is the formula of Chlor-a in Band Math of ENVI.

In addition Chlorophyll-a , we may use sea surface temperature from MODIS to get information distribution of phytoplankton in the ocean. if we combined both we may get great information...

nice to share :)

Best Regards,

Aji Putra Perdana

21 komentar:

  1. hello bung...........
    kok tutorialnya ga bisa di download semua.. sebenernya ada filenya ga sih? ato uploadnya ga clear.. cb di ceck lagi ya.. kasihan.. bagus komunikasi medianya tapi kurang di maintenance nya

  2. hello juga BUng..

    Untuk yang bertanya..maaf mohon dicek koneksi internetnya..

    tutorialnya ada...



  3. Tuk Anonim :

    Klik pada link tersebut. silahkan cari tulisan download apabila koneksi internet bagus maka artikel dapat didownload...

    Jika masih belum bisa, silahkan kirimi imel saudara.

    Jangan hanya emosi semata...Belajar bukan dengan emosi...Gunakan bahasa yang lebih baik..

    Salam hormat.
    Aji Putra Perdana

  4. APabila masih terdapat error, sila kirim imel saudara...


    Salam hormat.
    Aji Putra Perdana

  5. Naveed ahmad khan12 April 2010 14.03

    i visit your site n i got more information then other visited last month
    was good enough then last what i had gone throught

    online degree


  6. Bagaimana menentukan modis nDVIdan evi pada software envi dgn data L1b? Rumus sudah tau cuma bingung pemasukan formulanya pada envi..berkali2 ke band math error mohon bantuanya untuk belajar VIndeks. terima kasih

  7. dikoreksi dlu MODISnya...mungkin formulanya ada yang kurang pas

  8. salam...
    im doing my thesis, mapping potential fishing zone by using MODIS...could u pls help me...im just confusing in order to extract the image....to define the fishing zone, i used sea surface temperature and chlorophyl....

  9. salam...how to define the range of the sst n chlorophyll??i just confused.....

  10. to define the range, you may use simple classification or based on your fieldwork...

  11. ok.....after classification, it`ll be in class...am i right??then, how to define the sst or chlorophyll range for every classes??

  12. i used envi software tu extract the sst n chlorophyll...then i`ll save the image in tiff/geotiff....then, import to arcGIS...do u know how to process this image in arcGIS??

  13. it's better to save your file into erdas imagine (*.img). and if you already have arrange your color range in envi, usually you can directly got the colors if you open the file in arcgis

  14. if you already open your file (*.img) in arcgis you can use properties of the file and open tab symbology to arrange or define your class...

  15. o0oo...ok..thank for that info...=]

    i had followed the steps of yours in envi software in order to process the MODIS data...
    so now, i would like to produce map of potential fishing zone by using that images (sst and chlorophyll) in arcGIS....if u dont mind, could u pls give me some tips in order to map this image of sst and chlorophyll in arcGIS???

  16. o0ooo...=)

    i had combine the sst n chlorophyll by using Spatial Analyst Tools.

    after that, i used properties of combine image.
    i just confuse about the class and the readings...=(

  17. 1st you can reclass your sst and clor file, for example: into 25-27 degree celsius into class 1, then...bla bla...for exmple until 3 classes. and same for the clhor until 3 class

    you may create matrix.,..there will be nine. you can analysis which class that have the possibility for fishing ground

    then use spatial analysis tools to calculate or sum the sst and clor...

  18. adoyai.....sorry to say....=(
    but im still confuse...
    in envi software, after i apply the mask, i`ll used Isodata method to classify the SST or chlorophyll....then, the image will be in range of classes...let say, 20 classes.

    then, when i import to arcGIS software, the image will be in class....actually, how it is???

  19. i have to convert the image into vector format or not in arcGIS??

  20. you can save yous isoclass into *img file then you can open the image in arcgis.
    it's still in image
    or you may convert into vector file, then open it in arcgis

  21. ok...thanx a lot....
    i really appreciate it....