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SpotMap – Technical Specification

Technical Specification

SpotMap addresses the challenges of analysing 2D gels and Western blots. Images are quality checked on upload to address any potential challenges with the analysis. Positional variation in the spot patterns of the 2D gel and blot can make identification of corresponding spots challenging, alignment helps to overcome this. A single spot pattern is created to easily identify the corresponding spots on each image and results are clearly presented for easy reporting.

PC Specification

Windows Vista, 7, 8 and 10.
Recommended minimum: 4 GB RAM.
Performance is dependent on image file sizes.

SpotMap supports multi-core CPUs and 64-bit versions of Windows which are recommended for maximum performance.

Welcome to SpotMap, your essential partner for HCP coverage analysis via 2DE

SpotMap analysis features

Skip to: Images • Analysis • Align • Results • Data Access


What is images mode?

Images mode allows you to upload images to the project. On upload the images are quality checked and minor image edits can be performed.

What features are available in the Images mode?

  • Images are quality checked when uploaded to the project.
  • Minor edits are available in the main screen, including crop, flip and invert.
  • Additional editing tools can be found in the image editor.
  • Images can be given nicknames for easy identification.
  • Images are also labelled with short A, B, C tags for easy ordering and identification.

Available image formats:

We recommend using the following image file formats:

  • .tiff
  • .gel
  • .mel

SpotMap can also analyse data from these file formats:

  • .png
  • .jpg


What is Analysis mode? In the analysis mode, a master spot map identifying the location of all spots in the project is created. Spots on each image are then categorised as present or absent from this map. The present or absent settings are used to identify spots common, missing or additional to the images in a comparison and measure % coverage. What features are available in the analysis mode to create the master spot map?

  • Automatic spot detection with variable parameters for optimisation and easy re-detection of the initial spot map.
  • Spot editing tools including:
    • Select
    • Add
    • Merge
    • Split
    • Delete
    • Freehand edit
    • Draw spots
  • View and scroll multiple images simultaneously.
  • Create a filter to delete spots which meet certain criteria.

What features are available to categorise spots as present or absent

  • Set individual or an area of spots as present/absent using the coverage tools.
  • Use the new spot assignment option to set a default categorisation for all new spots.
  • Create filters based upon specific spot measurements to categorise spots as present or absent from the active image.

Other features available:

  • Add linear and non-linear pI scales to the project. The pI of each spot can then be estimated.
  • Add molecular weight scales to the images. The MW of each spot can then be estimated.
  • Relative percentage coverage compared to a selected base image is updated as the analysis is completed.
  • Investigate subsections of the image, including quadrants using the spot sets tool.
  • 3D view available throughout the analysis.
  • Secondary Image Display to enhance any visual distortions.


What is alignment?

Alignment takes two images and overlays them in the same coordinate space so that a spot on the image to be aligned will be in the same location as the matching spot on the target image. It makes it possible to accurately compare images by removing any positional variation introduced during the gel running, Western blotting and imaging processes.

How are images aligned?

Automatically generated or manually added vectors are used between features of the images to create a map between the images. If the images have very similar spot patterns this can be fully automated using our fast alignment algorithm. Where spot patterns differ some manual vectors are often required.

What features are available in the align mode to aid alignment?

  • Alignment can be completed automatically.
  • Manual vectors are added by simple click, drag and drop.
  • Individual or multiple vectors can be easily deleted.
  • The alignment vectors added to one image can be copied to another, this feature is particularly useful when used with DIGE techniques.

How can I visualise my alignment?

  • The align mode has four views to help you visualise the alignment:
  • Two colour full image view.
  • Two colour vector editing screen.
  • Transition window.
  • Checkerboard.
  • Variable colours and contrasts of the two colour displays.
  • Show the outlines of the spot map.
  • Show a grid to identify key areas of warping.


What is the results mode?

The results screen presents an overview of the percentage coverage and numbers of spots common and additional to the base image. There is a small heat map which identifies where the spots common, additional and missing are in relation to the whole image. Selecting “View Comparison” will open the base image and selected image in the analysis window in the colour scheme of Common, Additional and Missing spots. Results for spot sets can also be viewed in the results screen.

What features are available in the results mode?

  • Easily compare the results of coverage and spot numbers compared to the chosen base image.
  • View an overview heatmap of the location of spots common, missing and additional on the full image.
  • Selecting view comparison opens the selected image and the base image in the main analysis screen in the complex colour scheme for easy identification of those spots common, missing and additional.

Data Access

What is the Data Access window?

Data Access provides all the results, parameters and data of the project in one location for easy generation of a PDF report. It is accessed from the file menu. The information within the Data Access is grouped into the sub sets of Results, Images, Analysis Parameters, Other Info and Manual. All information can be added to reports and presentations by dragging and dropping or using the copy icon and pasting. Images and csv files can be exported directly into folders on the computer.

What data is available and how do I export it?

  • All data is exported into a readable PDF report using the generate PDF button.
  • An audit-trail can be generated using the audit-trail exporter tool this generates a complete audit trail straight from the software.
  • All data can also be exported by clicking the copy button and pasting into the desired location.
  • Data can also be exported by dragging and dropping into the desired location.
  • Data can be added to most locations, including Word, PowerPoint, and chosen file locations.

Host cell protein coverage example analysis report

Data Access

See what SpotMap can do for you:

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