Image and data upload: Difference between revisions
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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 push the "upload image and data files" button on the upper | 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 push 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 two single images (one for each channel) or one dualimage.For this click on the mentioined button.If you scanned the microarray with the Imagene software you have to upload '''two''' seperate data files, too. If you scanned with the [[GenePix]] software do '''not''' fill in the data file form for '''channel 2'''.For this click on the mentioned button, too. An error message will appear on top of the page if you submitted data in the wrong format or did not fill in all reqired fields. The fields that were filled in with the wrong data are highlighted in red. | ||
== Required fields == | == Required fields == | ||
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* Slide-ID, choose the microarray you scanned and you intend to upload images and data files for.(Make sure that you only choose a slide-ID that was assigned to you) | * Slide-ID, choose the microarray you scanned and you intend to upload images and data files for.(Make sure that you only choose a slide-ID that was assigned to you) | ||
* Date, the date the image and data files were uploaded | * Date, the date the image and data files were uploaded | ||
* Image type, whether single or dual image is uploaded. Default is single images | |||
* Scan software, whether imagene or genepix data file is uploaded.Default is Imagene | |||
* Pixel size, (has to be filled in, typically 10, default is "None") | * Pixel size, (has to be filled in, typically 10, default is "None") | ||
* Channel, the channel the microarray was scanned with (already filled in, default is "None") | * Channel, the channel the microarray was scanned with (already filled in, 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 image file, the path to the image file on your computer | |||
* Location of the data file, the path to the data file on your computer | * Location of the data file, the path to the data file on your computer | ||
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* Scan rate [%], the rate of scanning | * Scan rate [%], the rate of scanning | ||
* Remarks, remarks of the scanning process for an image | * Remarks, remarks of the scanning process for an image | ||
* Description, description of the data files | * Description, description of the data files | ||
Revision as of 16:27, 1 July 2005
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 push 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 two single images (one for each channel) or one dualimage.For this click on the mentioined button.If you scanned the microarray with the Imagene software you have to upload two seperate data files, too. If you scanned with the GenePix software do not fill in the data file form for channel 2.For this click on the mentioned button, too. An error message will appear on top of the page if you submitted data in the wrong format or did not fill in all reqired fields. The fields that were filled in with the wrong data are highlighted in red.
Required fields
The fields that have to be filled for the image upload are
- Slide-ID, choose the microarray you scanned and you intend to upload images and data files for.(Make sure that you only choose a slide-ID that was 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 images
- Scan software, whether imagene or genepix data file is uploaded.Default is Imagene
- Pixel size, (has to be filled in, typically 10, default is "None")
- Channel, the channel the microarray was scanned with (already filled in, 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 ArrayLIMSWiki: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 imagene and the genepix format. If imagene is used two data files has to be uplaoded. In case of the genepix format only one data file has to be uploaded.