Zoo/PhytoImage version 1.2-1 - ReadMe: ------------------------------------------- Installation notes: =================== 1) Make sure you run the ZooImage setup completely. This installs both ZooImage and PhytoImage. They share the same core code. Only the "skin" (external appearance, name, etc. of the program is different). 2) You should also install ImageMagick 16bit (run the ImageMagick-6.1.9-Q16-windows-dll.exe file that you can download from the ZooImage web site, or use the one provided on the ImageMagick web site (the 16bit version, not the usual 8bit version!). 3) Make sure, also to install Acrobat Reader version 5 or above to read the online version of the manuals and tutorials. 4) Download and install the various example data files from the ZooImage web site. No example dataset is provided any more with the default install in this version. Example datasets are useful for a first use of the software and to get an idea of the kind of image and metadata information you should provide to the software for your own analyses. So, do not overlook your training with the example datasets: plankton image analysis is a complex task, and consequently, ZooImage reflects somehow that complexity. Version notes: ============== Zoo/PhytoImage is a free software to analyze digital plankton pictures and it is also a general and flexible framework for developing such a kind of application (you can add your custom processes through plugins). Zoo/PhytoImage is constituted by a collection of independent software (R, ImageJ, XnView, SciTe, ...). To ease its installation under Windows (no version yet for Unix/Linux or MacOS X), everything you need is included in the setup. Zoo/PhytoImage is intended to be platform independent (it should run on Windows, MacOS, Linux and Unixes). However, at the current stage of developement, only the Windows version is available. Other versions for the other platforms will be available progressively, depending on collaboration we find from people willing to support these platform versions. To install Zoo/PhytoImage, you need 600Mb of free space on your hard disk. Also, a powerful processor (Pentium IV 3Ghz, or more) with 1-2Gb of RAM memory is required to process largest images. Currently, only a couple of plugins are provided in ImageJ (Plugins -> ZooPhytoImage menu): - Microscope Color. A plugin to process images coming from a microscope equiped with a digital camera. Scale must be measured separately for each picture (or at least, for each resolution used). Colors are not supposed to be calibrated. - Scanner Color. This is very close to the PVA 1.2 treatment. It works on Jpeg color images of stained fixed zooplankton (haematoxilyn) scanned with a simple commercial flatbed scanner in reflective mode (the usual mode). Just use a petri disk on top of the scanner to hold your sample. - Scanner Gray16. This plugin is designed to work with 16bit gray scale pictures scanned with an EPSON 4870/4990 flatbed scanner, or equivalent, in transparent mode with VueScan. - Macrophoto Gray16. A plugin to work with grayscale pictures obtained from macrophotography (tested with Canon EOS 20D and macro f2.8/100mm lens). The process is made as similar as possible to the Scanner Gray16 plugin. In the FIT submenu of ImageJ plugins, you can find also a version in development of FIT IMS, a plugin to process FlowCAM images and get results in a format fully compatible with Zoo/PhytoImage. This plugin is developed at Bigelow Laboratory by Mike Sieracki, Ben Tupper and collaborators. Of course, we are open to support more image types in the future: Zooscan, VPR, etc. but we need developers for such plugins. You can also adapt existing plugins to your particular needs (do not forget to submit general interest plugins for inclusion in future versions of Zoo/PhytoImage). You need also Acrobat Reader version 5.0 or above to read the manual that is in .pdf format (go to the Adobe web site at http://www.adobe.com to download and install a free version of the Acrobat Reader, if you need. Most software included in Zoo/PhytoImage can be used freely (they are under a GPL license, or similar, meaning you can freely use them, copy them and even change their code and redistribute your changes). This is the case of R, ImageJ, the SciTe editor (Sci1.exe), netpbm, ImageMagick, xite, zip/unzip/zipnote and dc_raw. Other software also included in this suite have more restrictive licenses. Make sure you read the respective 'license.txt' files in the corresponding directories and that your use of the software is in accordance with these specific license terms: - XnView is Freeware for private non-commercial or educational use, including non-profit organization (i.e. schools, universities, etc.) but not for commercial use (you must register the software before use). - VueScan is a Shareware, meaning you have to pay a (small) license fee and register before you can use it. - Filzip is a Freeware, but with a different license agreement than GPL. - DeepBurner is Freeware, but with advertisement for buying the full, commercial version of the product. In the future, it will probably be better integrated with Zoo/PhytoImage to automatically backup RAW images at will on DVD. Of course, you are free to use the software bundled with your own DVD burner instead. Zoo/PhytoImage team explicitly claims that Zoo/PhytoImage is mainly a collection of various software developed and licensed by their respective companies. Please, read the corresponding 'license.txt' and/or 'readme.txt' files. By using Zoo/PhytoImage, you accept and certify to respect all these respective license terms! For upgrades, new plugins and for getting an updated manual, visit the web site (http://www.sciviews.org/zooimage). For furthere questions or discussions, please use the forum (http://zooimage.overchord.net). We thank you for your interest in Zoo/PhytoImage. For the Zoo/PhytoImage development team Ph. Grosjean (phgrosjean@sciviews.org)