Review of Pedro's script work

[saloynton]

Meeting 24 January 2011
Present JM, Scott

The meeting was to provide an overview of Pedro’s script written against matlab tool and give an understanding of what preliminary steps can be made for integrating the tool with OMERO. The scripts work on either specifically in images or datasets as a whole.
(Outstanding notes will be taken from the tool screen shots.)

The set of main users for the scripts:

• Andy
• Keria
• Kim
• Nadal
• Annika (Pedro has spoken with about the possible use of the intensity analysis script.)

There was a comment on promoting the use of the scripts this will need to be considered at an appropriate point.

Script 1 – intensity analysis

• Workflow the image is selected from within the script > (need to confirm the workflow with Pedro/screenshot.
• Provides the ability measuring the volume of connecting ROI’s.

• This tool has the scope to provide the image-to-image link and so provide the ability to trace back to the original parent image.

Script 2 - Distant measurement

• Nadal specifically requested this tool.
• The script downloads the whole image this could become more problematic for future use.
• The workflow allows for the selection of the image > selection of the ROI’s required to measure between. (To clarify details with screenshot)
• If the metadata is provided from the server the script will provide the option to give the distance in microns.

Script 3 - Event timer

• Kim specifically requested this tool.
• The problem for the script was to gather the information between two time points in a movie.
• The workflow allows for the selection of the ROI around the chosen area
• The ROI’s are numbered
• The scope for the integration in Insight could be easier

Script 4 – (to confirm)

• This script was created for a scientists that eventually move away so has not been used.
• The script allows for the measurement of the angle within the cell to be fixed and then measured through the time frames.

Script 5 - Frap scrip

• This script is set out to solve the issue of the movement of the centre of the image during the frap experiment so preventing loss of any data.
• The script allows for 2 ways of working:

1) tracking the centre of the image using the mouse pointer.
2) using the mouse click to follow the image centre.

• The script allows for the adjustment of time between clicks to allow for easier use and for the pause of the clicking by pressing esc.

Script 6 – Boxit

• The script allows the ROI to be snapped around the object.
• The script allows for the reduction of lenses flares, allowing the user to select out the extra information.

Script 7 – Label maker

• This tool is a labelling tool for scientific images.
• The workflow allows the user to label images i.e. mitosis. > once completed a batch analysis of all the labels can be calculated.
• The labels can then be shown per image, across z sections, percentage labelled.

The meeting in #3859 and subsequent User story defined for the investigation #3913 is relevant for this script.