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  • Just getting started with Zooscan...
    copepods just to get an idea of how things work I have gotten the sample scanned and Zooscan has placed outlines and numbers around my copepods However it does not seem to be saving the images as vignettes I m not exactly sure where to go from here I know it s hard to explain these things in a paragraph but I thought I d give it a shot Any information you could provide would be greatly appreciated Thanks benmcg Posts 4 Join date 2010 04 19 Getting started with Zooscan Zooprocess system picheral on Thu Apr 22 2010 3 50 pm Hi You should read the short manual now available onto the website If you do not enable the option to extract vignettes after the process you do not get any vignette The standard procedure is 1 Create project using default parametres select only the proper scanning option for frame size and resolution 2 Scan background when you start every day 3 Convert and Process in batch 4 Check process using on of the available methods Then you can start with Identification using the dedicated tools You can also read the recent publication from Gorsky in JPR about the

    Original URL path: http://zooscan.forumakers.com/t52-just-getting-started-with-zooscan (2016-02-14)
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  • Windows x64
    the UI of ImageJ and Zooprocess We are talking about installing 64bit Windows XP and have received word that the vuescan software will work fine with that Are there any limitations in the IamgeJ Zoprocess software in relation to this Jon Jonern Posts 7 Join date 2008 09 09 Similar topics Similar topics Has Anyone Gotten Chrome Driver to Work with Windows 7 Selenium RC with Google Chrome on Windows

    Original URL path: http://zooscan.forumakers.com/t51-windows-x64 (2016-02-14)
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  • Data Management of projects
    important sample meta txt a copy of the metadata file from the raw folder anything changed sample msk1 gif the mask file obviously needs to be kept sample out gif inverted downscaled image Not sure what its used for but its not huge so no problem in keeping this sample vis1 zip a relatively large 156MB in my case file Looking at the compression ration it looks like this is a zipped version of the 8 bit image from the scan folder Are both necessary Altogether each scan eands up eaching around 1 8 GB and I m jsut wondering if there s a way of trimming the active projects i m working with I will always keep a raw backup of the original scan project so I m not too worried about loosing information but if it could be made a little lighter to swap orojects between computer network and external HDD s it would shave quite a bit of time of and if the usage of network storage can be reduced slightly it would also be a benefit since this is much more expensive I m interested in hearing how others are handling the juggling of these large projects I have about 9 years projects of 100GB each to work on with 160 200 scans in each so even if its something simple that saves a couple of hours on each project it all adds up to quite a bit of time saved jensr Posts 8 Join date 2008 09 26 Age 41 Location Marine Scotland Science Aberdeen UK Re Data Management of projects jensr on Thu Feb 04 2010 3 12 pm From the manual p32 The RAW images created by Vuescan if you select the save 16 bit raw image option are saved uncompressed in the raw folder with their respective meta and log files The conversion tool described below can Zip the Tif images automatically default option Users will have to remove the original Tif images manually after the conversion as Zooprocess will never delete any file The Tif images can also be compressed using Winzip or preferably Power archiver http www powerarchiver com which allows batch file compression If you use this last method the zip file naming will differ from the single archive compression Zooprocess can handle both archives names You must NOT compress the meta and the log files From that I m taking it that it is ok to remove the sample raw tif once the processing is done if I used the raw images I guess the main confusing for me is the creation of the zip file in the raw folder in the first place Does this zip file actually serve any purpose or is it used at any stage in the processing It s the swap between the raw tif file and the zip file in terms of processing I m uncertain about at this stage On page 40 of the manual 6 15b it says The raw

    Original URL path: http://zooscan.forumakers.com/t50-data-management-of-projects (2016-02-14)
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  • Odd mask files after processing
    the mask file it seems something very odd has happened during the conversion or background subtraction The background scan looks clean So I m wondering if this is a processing setting of if we have a nother major problem with the scanner jensr Posts 8 Join date 2008 09 26 Age 41 Location Marine Scotland Science Aberdeen UK Pb with background picheral on Sun Nov 22 2009 10 55 pm Dear Jens I had a look at your images They are apparently OK but I know that the eyes are much more adaptable than the machines I would like to get the image and associated files to check the process on my side and understand the reason which prevents a good background removal Regards Marc P picheral Posts 60 Join date 2008 05 02 Re Odd mask files after processing jensr on Thu Nov 26 2009 12 22 pm Just in case anyone has experienced similar problems Marc is currently looking over some of our images so a final verdict is pending But in the meantime I have reprocessed the sample set using the rolling ball background method instead and it has improved the process enormously jensr Posts 8 Join date 2008 09 26 Age 41 Location Marine Scotland Science Aberdeen UK Background subtract on Zooscan from Aberdeen picheral on Mon Dec 07 2009 5 35 am Hi Jens The background subtract problem arises when the optical properties light calibration of the systems have either not been well adjusted in factory or modified by user Your Zooscan comes from the first series from Biotom Company As you opened your machine and modified the internal calibration strip the cover light probably needs an adjustment to provide an easy background subtraction This must be done by expert but the Biotoms models are

    Original URL path: http://zooscan.forumakers.com/t49-odd-mask-files-after-processing (2016-02-14)
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  • Error when processing in batch mode
    error message This suddenly became a problem Jonern Posts 7 Join date 2008 09 09 More error Jonern on Thu Oct 08 2009 3 27 pm Today after teaching one of my colleagues how to scan samples I startet the processing in batch mode to show him how The processing didn t even start before an error message came up What can this be jOn Jonern Posts 7 Join date 2008 09 09 Solutions or Error in processing in batch mode picheral on Sun Oct 25 2009 11 19 am Dear Jonern As most users you do not give much precision on the circumstances Looking at the images you posted I would recommend to check that the log file from the raw folder is not corrupted Compare it with another in the same folder or from another folder If you cannot success to process your sample please contact me by email I will send you an FTP adress to post the 3 files from the raw folder log tif meta plus the related background files ALL from the day you scanned your sample Regards Marc P picheral Posts 60 Join date 2008 05 02 Similar topics Similar topics Element not

    Original URL path: http://zooscan.forumakers.com/t48-error-when-processing-in-batch-mode (2016-02-14)
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  • Error message during single image processing
    0 8 4 0 1 3 0 05 0 1 10 both Image process Zooscan 1asep Version 6 10 Picheral CNRS Image path H Zooscan stn mr350 Image stn 2000 05 29 497 a1 1 tif Frame 1 Raw image depth 8 bits Raw image size 365051090 Raw Image BackUp as ZIP NO Final Image 8bits Corrected width 24272 Corrected heigth 15040 Grey Level Adjustement YES Resolution 2400 ODxminref 23979 ODyminref 7367 ODxdimref 60 ODydimref 600 OD measured 77 Max min grey difference in OD 19 STD 2 1085 OD correction NO Background correct using 20090708 0932 background large manual tif Image treatment natural Right side Automatic supress Right side Limit 23273 Transparent frame CLEAR Greytaux 0 9 Greylimitright 168 Right limit 23162 Greylimitrleft 200 Left limit 84 Greylimittop 171 Upper limit 172 Greylimitbottom 147 Bottom limit 14678 Vis image save YES Particules Process Particule Process Date 20090903 1417 Version 5 00 2006 12 29 Picheral CNRS ConfigDataP last no created 20090707 1441 100 0 4 2400 0 9 0 150 2 0 025 0 25 2 0 20 0 0 neutral 243 174 1 1 1 pixel 100 0 0 3 100 1 0 0 3383 4 2852 16 0 8 4 0 1 3 0 05 0 1 10 both Resolution 2400 Calibration created 20090707 1441 Threshold 243 PixSize 0 0106 MinSize 0 3 MaxSize 100 Method default 0 3000 100 Measures unit pixel Min Area 631 Max Area 70120652 Separation Mask UNUSED Particle Analysis YES Analysis Method from thumbnail images fractalA skeleton Slope Histcum Mg5 Complexity Symetry Particle Analysis ABORTED Analysed Objects 0 TAG NO Results SAVED Date 20090904 0906 Last edited by jensr on Fri Sep 04 2009 1 16 pm edited 1 time in total Reason for editing fixed typo s jensr Posts 8 Join

    Original URL path: http://zooscan.forumakers.com/t47-error-message-during-single-image-processing (2016-02-14)
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  • Efficient method for creating separation mask?
    potentially very time consuming For example we have found that if we use the separation using vignettes function if we wish to save our work and return to the image to continue processing the next day we have to page through all of the vignettes that we have already corrected made any necessary cuts to and with approximately 1000 vignettes per image this is time consuming Likewise we have found that if we process the converted image with the selection to create the separation mask if we choose to stop the process and save the results we cannot return to the same image and continue the analysis and it is a little worrisome to leave work unsaved to avoid this issue We are seeking any advice that experienced users may have It is entirely likely that we are not aware of some features of the Zooprocess software or that we are simply faced with some messy samples that require more work I should note that these samples are from a historically important time series and we are exploring if we can create a digital archive of the entire sample While the sample volume is not terribly large due to some of the smaller organisms present we are splitting to 1 32 and it is not really feasible to split any further We have also explored size fractionation but that had some issues as well and is not a good option for these samples Any advice would be welcome as we decide how to proceed Malinda Sutor msutor Posts 6 Join date 2009 03 12 Separation methods and strategies picheral on Fri Aug 28 2009 10 31 am Dear Malinda I agree that this separation is very time consuming As you mentionned it is also necessary to separate some samples anyhow

    Original URL path: http://zooscan.forumakers.com/t46-efficient-method-for-creating-separation-mask (2016-02-14)
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  • Zooprocess does no longer start.
    at all for several days Thanks Alison My response Dear Alison Very few details can help much The zooprocess txt file which is in your zooscan root directory is probably corrupted Make a copy of it and try to edit it It must contain ONLY the list of the directories of your projects You must keep AT LEAST two lines and remove all the characters that may stay after the last line Here is the copy of the file on my laptop E Zooscan scor lsu E Zooscan test rectangles E Zooscan scor lsu E Zooscan sanaetest You notice that one line is writen both on top of the file and somewhere else The top line is the folder of the project that was last utilized by the last user of Zooprocess If you must remove the file You will have to reset the Zooscan parametres before importing your project Good luck Marc P picheral Posts 60 Join date 2008 05 02 finally a solution LAPS on Tue Aug 18 2009 4 31 pm Thank you Marc you have put us on the right trail We were desperate with Zooprocess not starting anymore on two computers Re installing the root folder did solve the problem Greetings from Luciana and Sabine LAPS Posts 7 Join date 2008 05 06 Why Zooprocess sometimes do not start How to prevent the problem picheral on Fri Aug 28 2009 10 19 am As most of you noticed yet Zooprocess does not start when the zooprocess txt file is corrupted It is easy to correct the file and import the lost projects How to prevent this The zooprocess txt file is corrupted when you start twice Zooprocess on your computer by clicking twice on the Z icon on the ImageJ menu be carefull with this

    Original URL path: http://zooscan.forumakers.com/t42-zooprocess-does-no-longer-start (2016-02-14)
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