Picking

In the Picking step, you can export spots to a pick file that can be read by a spot excision robot. To do so, you first select an image to pick from, align it to an experiment image if needed, choose spots for picking and finally export the pick list.

How to

Select and edit the image to pick from

First choose an image to pick from in the Image to pick box. You can choose an image from disk, or pick spots on one of the experiment images.

If you pick from one of the experiment images, you can immediately choose spots for picking. If you imported a pick gel from disk, you may need to edit the image and align it to one of the experiment images.

Under the Edit image to pick icon, you will find the following tools to edit the pick image:

  • Adjust Contrast
  • Rotate left
  • Rotate right
  • Flip horizontally
  • Flip vertically
  • Invert gray levels

Align the pick image to an experiment image

You can use the options under the Alignment icon, as well as the Align tool, to align your pick image with the experiment image. Their functionality is described in the Alignment step.

You can warp/unwarp your pick gel, or show/hide match vectors with the corresponding options under the Alignment icon.

Choose spots for picking

You can choose spots to pick in various ways. The spots selected for picking are shown in violet on the images and will be listed in the Spots to pick table at the bottom of the screen.

PickMode Pick

Manually choose spots for picking using the Pick tool.

ChooseSpotsPick Choose spots to pick

Click Choose spots to pick to select a spot set or annotation category to pick spots from, or to select a list of spots that you have validated for a particular analysis (specified by the Analysis-ID), or for the entire experiment (Validation).

ExcludeIcon Clear all spots to pick

Click Clear all spots to pick to clear the list of spots to pick.

Export the pick list

Finally, you can choose the options for your pick list export.

  • Type – Specify the spot picker and format. The available options are:
    • Generic
    • GE Healthcare Ettan (XML)
    • GE Healthcare Ettan (Text)
    • Genetic GelPix
    • Genomic Solutions Propic
    • Bruker Proteineer SP (XML)
    • Bruker Proteineer SP (Excel)
  • File – Enter a file name and specify the folder where the file should be saved.

Depending on the Type you selected, other information may be requested:

  • Units – Specify the units in which the coordinate data shall be saved.
  • Ettan markers – For the GE Healthcare Ettan exports, identify the two Ettan markers that were placed on the gel before scanning. To specify the marker positions, click the Ettan marker tool and first double-click the center of the left marker. Then double-click the center of the right marker.

Click Generate file to confirm the pick list export.