Image and data upload: Difference between revisions

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=Image and data upload=
This page shows all images and data files that were uploaded for the microarray hybridizations in your project. If you want to submit new images and data files for a scanned hybridized microarray click on the "upload image and data files" button on the upper left side of the page. Fill out '''every''' field marked with a red star ('''required fields''') on the opening page. You are able to upload either two single images (one for each channel) or one dual image. In each case, click on the corresponding button. If you have scanned the microarray with the Imagene software you have to upload '''two''' seperate data files aswell. If you have scanned with the GenePix software do '''not''' fill out the data file form for '''channel 2'''. In this case click on the mentioned button, too. An error message will appear on top of the page if you have submitted data in the wrong format or did not fill out all required fields. The fields that were filled out with the wrong data will be highlighted in red.


This page shows all images and data files that were uploaded for the slides in your project. If you want to submit new images and data files for a scanned hybridized microarray push the "upload image and data files" button on the upper right of the page. Fill out  '''every'''  field marked with a red star (  '''required fields'''  ) on the opening page. You '''always''' have to upload '''two''' images (one for every channel). If you scanned the microarray with the imagene software you have to upload '''two''' data  files too. If you scanned with the genepix software do '''not''' fill the data file form for '''channel 2'''. Just fill out the data file form for'''channel 1''' .An error message will appear  on top of the page if you submitted data in the wrong format or did not fill all reqired fields. The fields that were filled with the wrong data are highlighted in red. Please notice, that select boxes have to be set again after submitting wrong data.
== Required fields ==


==Required fields==
These are the required fields that have to be filled out for image upload:


The fields that have to be filled for the image upload are
* '''Slide-ID''': choose the microarray you have already scanned and which you intend to upload images and data files for. (Make sure that you only choose a slide-ID that has been assigned to you)
* '''Date''': the date the image and data files were uploaded
* '''Image type''': whether single or dual image is uploaded. Default is single image
* '''Scan software''': whether Imagene or GenePix data file is uploaded. Default is Imagene
* '''Pixel size''': the pixel size of the uploaded images (has to be filled out, typically 10, default is "None")
* '''Channel''': the channel the microarray was scanned with (already filled out, default is "None")
* '''Location of image file''': the path to the image file on your computer. Note that only Tiff-format is allowed
* '''Location of the data file''': the path to the data file on your computer


* Slide-ID, choose the slide you scanned and you want to upload images and data files of.(Just choose a slide that were assigned to you )
== Optional fields ==
* Date, the date the images and data files are uploaded
* Pixel size, (always filled, Default is "None")
* Channel, the channel the microarray were scanned with (is already filled, Default is "None")
* File format, the format of the image. Usually it is .tiff (is already filled. Default is tiff)
* Location of image file, the path to the image file on your computer
 
The fields that have to be filled for the data file upload are
 
* Used software, the software the microarray was scanned with (is already filled, Default is "None")
* Location of the data file, the path to the data file on your computer


== Optional fields ==
You can also upload some additional data for the images:


You can also upload some additional data for the images
* '''Laser power [%]''': the power of the laser used for microarray scanning
* '''PMT [%]''': the photomultiplier values
* '''Scan rate [%]''': the rate of scanning
* '''Remarks''': remarks of the scanning process for an image
* '''Description''': description of the data files


* Laser power [%], the power of the laser the microarray was scanned with
=== File formats ===
* PMT [%]
* Scan rate [%]
* Remarks, remarks of the scanning process for an image


You can also upload some additional data for the data files
The format for the image files the [[ArrayLIMSWiki|ArrayLIMS]] system allows is the '''Tiff''' format. Because of its non-lossy compression it best suits the purpose of scientific work.


* Description, description of the data file
The supported format for the uploaded data files are the corresponding Imagene and the GenePix formats. If Imagene is used, two data files have to be uploaded. In case of the GenePix format, only one data file has to be uploaded.
* Normalized, wether the image was normalized or not (already filled. Default is " -No- ")
* Filtered, wether the image was filtered or not (already filled. Default is " -No- ")

Latest revision as of 07:16, 26 October 2011

This page shows all images and data files that were uploaded for the microarray hybridizations in your project. If you want to submit new images and data files for a scanned hybridized microarray click on the "upload image and data files" button on the upper left side of the page. Fill out every field marked with a red star (required fields) on the opening page. You are able to upload either two single images (one for each channel) or one dual image. In each case, click on the corresponding button. If you have scanned the microarray with the Imagene software you have to upload two seperate data files aswell. If you have scanned with the GenePix software do not fill out the data file form for channel 2. In this case click on the mentioned button, too. An error message will appear on top of the page if you have submitted data in the wrong format or did not fill out all required fields. The fields that were filled out with the wrong data will be highlighted in red.

Required fields

These are the required fields that have to be filled out for image upload:

  • Slide-ID: choose the microarray you have already scanned and which you intend to upload images and data files for. (Make sure that you only choose a slide-ID that has been assigned to you)
  • Date: the date the image and data files were uploaded
  • Image type: whether single or dual image is uploaded. Default is single image
  • Scan software: whether Imagene or GenePix data file is uploaded. Default is Imagene
  • Pixel size: the pixel size of the uploaded images (has to be filled out, typically 10, default is "None")
  • Channel: the channel the microarray was scanned with (already filled out, default is "None")
  • Location of image file: the path to the image file on your computer. Note that only Tiff-format is allowed
  • Location of the data file: the path to the data file on your computer

Optional fields

You can also upload some additional data for the images:

  • Laser power [%]: the power of the laser used for microarray scanning
  • PMT [%]: the photomultiplier values
  • Scan rate [%]: the rate of scanning
  • Remarks: remarks of the scanning process for an image
  • Description: description of the data files

File formats

The format for the image files the ArrayLIMS system allows is the Tiff format. Because of its non-lossy compression it best suits the purpose of scientific work.

The supported format for the uploaded data files are the corresponding Imagene and the GenePix formats. If Imagene is used, two data files have to be uploaded. In case of the GenePix format, only one data file has to be uploaded.

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