Wish List For CalcImage

[Ben Buse]

Hi

Whilst acquiring some great MAN quant maps, with user able to process on own computer, a query arose.
User doesn't have golden software surfer to export them. Which left user dependent on the ascii export or using gdal to read grd (which are great if you like scripting or inputting into your favorite package for plotting).

 As far as I'm aware in calcimage whilst you can export the maps as bmp, you can't overlay scale bar and colour intensity scale, or choice the color range. I just wondered if there was a way to create within calcimage an easy map export without surfer, to generate an image file with the necessary information on it

[John Donovan]

Whilst acquiring some great MAN quant maps, with user able to process on own computer, a query arose.
User doesn't have golden software surfer to export them. Which left user dependent on the ascii export or using gdal to read grd (which are great if you like scripting or inputting into your favorite package for plotting).

 As far as I'm aware in calcimage whilst you can export the maps as bmp, you can't overlay scale bar and colour intensity scale, or choice the color range. I just wondered if there was a way to create within calcimage an easy map export without surfer, to generate an image file with the necessary information on it

There are several options for exporting images from CalcImage without using Surfer.  Here is a topic that discussed this a few years back:

https://smf.probesoftware.com/index.php?topic=997.0

1. First of all note that registered students can get access to Surfer to ~$50 per year:

https://www.goldensoftware.com/solutions/education/

2. One can import the "Classify" ASCII .DAT files into another application, for example ImageJ.  I believe that several users who process hundreds of quant maps at a time, have written scripts for this.  Maybe they will post their scripts to this topic...

3. We have also hired a developer to create a standalone app for basic output of quant maps with optional axis marks, and a scale bar and data color scale.  This will hopefully be available later this summer.  This will just be for basic image output. For full customizable presentation output of quant maps, we will still utilize the Golden Software Surfer application's extensive scripting capabilities.

[Ben Buse]

Not sure if this is the right place,

But it's cool what Paul Carpenter does with scripts and Open Sea Dragon to create QME Tool, so that a quant map can be hosted on the web, interactive so can select element, RGB colour, can extract quant data from single point or an area.

Seems like a fantastic way for open science, once mapped a rock, don't need other labs to map it again, just share it in this way, great for collaboration, great for building up knowledge database.

Maybe a long term project would be creating a way of exporting calcimage data to a similar interactive web-based format

[John Donovan]

But it's cool what Paul Carpenter does with scripts and Open Sea Dragon to create QME Tool, so that a quant map can be hosted on the web, interactive so can select element, RGB colour, can extract quant data from single point or an area.

Seems like a fantastic way for open science, once mapped a rock, don't need other labs to map it again, just share it in this way, great for collaboration, great for building up knowledge database.

Maybe a long term project would be creating a way of exporting calcimage data to a similar interactive web-based format

Yes, Paul's Quantitative Map Explorer (QME) is very cool. In fact we've offered to host a forum board here for the software with him as moderator, but he wants to hold off until they finish a few more features.

Right now Paul just loads the Classify DAT files exported from CalcImage into QME and one can start "exploring"!   

[Ben Buse]

Yes, Paul's Quantitative Map Explorer (QME) is very cool. In fact we've offered to host a forum board here for the software with him as moderator, but he wants to hold off until they finish a few more features.

That would be good, it be great to be able to give it a go

[John Donovan]

Yes, Paul's Quantitative Map Explorer (QME) is very cool. In fact we've offered to host a forum board here for the software with him as moderator, but he wants to hold off until they finish a few more features.

That would be good, it be great to be able to give it a go

I would write Paul directly and ask that he allow others to utilize his QME web site for their own maps.

[Paul Carpenter]

John and Ben,

First of all, the QME tool is "Quantitative Microanalysis Explorer" and we use "Q-tool" for short since obviously people are not able to remember the name   ... Please use The Google to see references to publications to date.

I am currently working on moving the code from Matlab to Python. I am in the process of discussing with Ryan Ogliore and Brad Jolliff where we go with the tool. We favor open source but there are discussions needed and some issues with development under NASA and WashU funding, etc.

I would like to work on dovetailing with the CalcImage output as I have talked to John about several times, and have been working on code to make this happen.

The other aspect is Python coding using PyImageJ to interface with Fiji. That allows interrogation of quantitative map stacks and using the tools that are designed for image analysis.

The QME tool currently uses the web browser which is very nice for collaboration and I am looking at Python coding which allows the html scripts to be written.

Yes, currently it is a multistep process. What is really needed is the ability to take an EDS datacube and extract spectra, quantify, and present analytical data on demand. This could be done immediately after a map frame is acquired.

Stay tuned.

Paul

[John Donovan]

First of all, the QME tool is "Quantitative Microanalysis Explorer" and we use "Q-tool" for short since obviously people are not able to remember the name   ... Please use The Google to see references to publications to date.

Sorry about that! "Quantitative Microanalysis Explorer" is even better but it is a mouthful! I will call it "Q-tool" from now on.