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  • ImageJ memory problem: another solution
    during image process period Macro error Macro editor not available in line 12 As suggest by some in the IJ wiki there are other alternative JVM that have no memory limitations on 32 bit win xp The one we found is Jrockit originally by BEA After install we modified the ImageJ cfg file in IJ root folder change the second line into the directory that contains the newly installed javaw exe for example C Program Files Java jrockit R27 5 0 jre1 6 0 03 bin javaw exe After this we can start IJ with memory set to 1640MB or more and finish all batch processes Cheers Chang EcoInformatics Lab http homepage ntu edu tw complex ecoinformatics c html Chun yi Chang Ted Ecoinformatics Lab Institute of Oceanography www oc ntu edu tw National Taiwan University Tel 886 2 3366 9746 ChangCY Posts 6 Join date 2008 05 29 Memory limitation issue reolved sylvain on Mon Aug 03 2009 6 36 pm We performed the upgrade here at Hydroptic and it did work Here is the link to JROCKIT on Oracle web site http www oracle com technology software products jrockit index html Select Oracle JRockit Mission Control 3 1

    Original URL path: http://zooscan.forumakers.com/t43-imagej-memory-problem-another-solution (2016-02-14)
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  • Background scanning resolution
    it only works if the background is scanned at 1200 dpi Maybe I have missed something on the manual or from your explanations in Baton Rouge Many thanks Rubens Lopes rmlopes Posts 4 Join date 2008 05 30 Background scanning resolution picheral on Mon Aug 10 2009 7 43 pm Dear Rubens The background must be scanned and normalized as the samples are except for the resolution The manual never say that you have to adjust the background resolution anyhow If you carefully check the vuescan screen you will see that the background is scanned at 1200 and saved at 1 4 of this resoulution leading to 300 dpi background in ALL cases Keep everything as it is by default in Zooprocess Best regards Marc P picheral Posts 60 Join date 2008 05 02 memory problem rmlopes on Mon Aug 10 2009 8 59 pm OK Marc not a problem Is this because of memory limitations on ImageJ Kind regards Rubens rmlopes Posts 4 Join date 2008 05 30 Background scanning resolution memory limitation picheral on Wed Aug 12 2009 11 56 am Dear Rubens Yes I tried to reduce the size of the background files as much a s

    Original URL path: http://zooscan.forumakers.com/t44-background-scanning-resolution (2016-02-14)
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  • Profile - rmlopes
    FAQ Search Search Query Display results as Posts Topics Advanced Search Memberlist Usergroups Register Log in Current date time is Sun Feb 14 2016 7 18 pm Viewing profile rmlopes Visitor messages Profile Statistics Contact All about rmlopes Posts 4

    Original URL path: http://zooscan.forumakers.com/u17 (2016-02-14)
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  • How to correct a prediction (using vignettes), How to work with large datasets
    Malinda As I explained in Baton Rouge last May we have defined a strategy to help work with thousands of vignettes we predict in batch of samples containing up to 10000 vignettes at all We use enable the detailled files in PKId and to save the results of the analysis in the Pid results Prediction directory of the project We also use to name the prediction Analysis date time which will be automatically added to the resulting files after being predicted these PID files are manually moved into the pid predicted directory inside the pid result folder It prevents to predict them again and validate them again we extract vignettes accordind to prediction into the date time to validate directory The dat1 txt files are automatically copied into the date time to validate directory and into the dat1 extracted subfolder of the pid results folder 6 12 You thus know which dat1 txt file have been extracted for validation the vignettes extracted in the to validate directory are validated by expert sorted in the correct folder or in more folders for a detailled sorting We utilize xnview exe for that but you can also utilize the Leaning set tool in Plankton Identifier providing that you copy the PID files in the date time to validate folder Most care must be applied to avoid loosing any vignette if you do not utilize PKId when the sorting is finished we use to rename the folder date time to validate by date time validated by expert name This is not mandatory but very usefull for the superviser of the work we then utilize either PKId to create what is called a TEST FILE see PKId manual or the Zooprocess Load Id from sorted vignettes to update the dat1 txt files with the new validated Ids The latest version of the tool 6 12 copies also the validated dat1 txt files into the dat1 validated sub directory of the pid results folder All the dat1 txt or txt files are thus 6 12 updated inside the dat1 validated of the pid results folder insuring that these files have been validated and that user knows exactly which files have been validated Checking the pid predicted the dat1 extracted and dat1 validated directories you can know exactly what has been processed The major difference beetween PKId and Zooprocess is that PKId works creates a new learn pid file containing the variables and the validated Id for each of the object Zooprocess can upload the validated Ids either in any txt file issued from the prediction including the analysis txt file or in the detailled dat1 txt files if the option to process detailled results has been enabled in PKId In Villefranche we utilize both strategies but we now prefer to work with dat1 txt files as they will contain log information of the image process metadata variables prediction and validated Id for each of the objects In addition to this the Upload Ids from sorted vignettes

    Original URL path: http://zooscan.forumakers.com/t41-how-to-correct-a-prediction-using-vignettes-how-to-work-with-large-datasets (2016-02-14)
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  • Computer for Zooprocess
    requires Windows Xp x64 512 Mo are sufficient to process any size of 1200 dpi images See chapter 3 4 2 4 to check if your computer has the sufficient image memory to process the highest quality images 2400 dpi A 1280 x 1024 monitor is a minimum We recommend 1680 x 1280 for better image viewing The computer should have a good graphic card not embedded onto the main board This computer must be operated with Xp pro SP2 A mouse fitted with a roll button is requested for most of the manual graphic tools measurements tag separation identification vignette display from graph Note ZooProcess is developed and tested only on a regularly updated Windows XPpro SP2 OS 32bits We do not plan to set it for Vista for the moment 2008 02 We recommend to install the computer OS on a small 10 15 Go boot hard drive C or D The computer should have at least an additional large capacity hard drive for images D or E On some computers we observed that a requirement is in the order of the drives the CDROM letter appears in the last position i e F Otherwise you may have an error message when launching the ZooProcess macro We also recommend keeping the Zooscan computer free of software that is not requested for the Zooscan operation and checks This is the simplest way to avoid any conflict with ImageJ and Java The application notes at this URL http www obs vlfr fr LOV ZooPart ZooScan rubrique php3 id rubrique 36 lang en give some responses There is no final answer today The major issues are related with ImageJ I do not have any recent PC to test Zooprocess today but the results obtained by Fabien on its laptop last year show that there might be solutions for bi proc PC Marc P picheral Posts 60 Join date 2008 05 02 Computer dual core issues picheral on Mon Apr 06 2009 11 02 am Question from Yianna We are in the process of setting up the Zooscan we have here at the Oceanography Centre model type ZSCA02 serial no 017 and we have a question regarding the computer that we need to purchase Is it possible to install the Zooprocess software and use the Zooscan with a dual core processor computer The Zooscan hardware user manual v 1 2 0 we have emphasizes that bi processor computers are not compatible with Zooprocess Is this still the case or with the new version of Zooprocess a bi processor can be used Would a computer with newer specifications than the ones given in the manual still work without any problems with Zooprocess 6 01 or Zooprocess 5 12 Also on another note do you have any news on when you are planning the next Zooscan training session Thanks Sincerely Yianna Dear Yianna I cannot respond to this precise question as we have no dual core processor PCs in our team I have no

    Original URL path: http://zooscan.forumakers.com/t21-computer-for-zooprocess (2016-02-14)
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  • Error using "View vignettes" with 6.10
    narrow frame images and with images that were converted and processed with an earlier version of Zooprocess and with 6 10 Other functions such as Viewing the Segmented Image and Separation by Vignette appear to work fine Is anyone else experiencing this issue msutor Posts 6 Join date 2009 03 12 View vignette error in version 6 10 picheral on Tue Jun 09 2009 7 32 pm Dear Malinda This view vignettes bug is fixed in version 6 11 Your email question I have read the installation instructions and one question that I had is once I have installed the new Image J Zooprocess etc can I put my old project folders back into the root folder or should I keep them separate Thank you Once I have completed the software upgrade and worked through processing a image using Plankton Identifier and then returning to Zooprocess to extract the vignettes and validate the results I will see if I still have any questions and I will post them to the forum Thank you The upgrade is very easy You don t have to care about anything else than placing the new macros in the ImageJ macros directory All the Zooprocess

    Original URL path: http://zooscan.forumakers.com/t39-error-using-view-vignettes-with-6-10 (2016-02-14)
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  • Extracting vignettes, we get blank vignettes and black vignettes
    be around 50 to 60 of these bad vignettes out of 1000 There are still measurement for those vignettes in the PID file so I suppose this problem occurred during the extracting procedure We are using Zooprocess 5 07 for a long time already Any way to fix this Thank you Ted ChangCY Posts 6 Join date 2008 05 29 Similar topics Similar topics How to take the screen shot

    Original URL path: http://zooscan.forumakers.com/t38-extracting-vignettes-we-get-blank-vignettes-and-black-vignettes (2016-02-14)
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  • zooprocess 6.10 download
    web has empty subfolders for zooprocess and zooscan install And I m not really sure what to do with Zooprocess version 6 10 zip that i also downloaded from the web as it contains no exe files yianna Posts 2 Join date 2009 05 18 Location Nicosia Cyprus Installing Zooprocess picheral on Mon May 18 2009 3 44 pm Dear Yianna Please follow the steps described in the manual http

    Original URL path: http://zooscan.forumakers.com/t37-zooprocess-6-10-download (2016-02-14)
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