Re: ObjectJ

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Re: ObjectJ

Frances Elizabeth Barron
Hi All,

I've attached a sample image of what I'm trying to measure. I am not sure if this is the best way of doing this, but I'm trying to measure the area and incidence of the labeled vessels in multiple sections. The goal would be to try and see if there is an increase in size or number of vessels between control and knockout animals. I have downloaded ObjectJ and used this to draw ROIs around the labeled vessels, then calculate area from that after specifying pixels/distance, which I calculated from a scale bar and Photoshop. The questions I have are:

1) Is there a better way of doing this? We are working on trying to set up confocal, but are having antibody penetration issues. So, for now, we are assessing multiple sections through the structure, normalizing to size, and calculating as described above.
2) Is there a way to save an image of the ROIs to show how the regions were drawn?
3) How exactly is the area calculated within a user defined ROI and what are the output units?

Appreciate the help and explanation for a newbie.

Best,
~Francie

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Francie Barron, Ph.D.
Postdoctoral Fellow, Joseph Wu Lab

Stanford University School of Medicine
Lorry I. Lokey Stem Cell Research Building
265 Campus Drive, Room G1105
Stanford, CA 94305-5454

Phone: (650) 724-5564 or (650) 724-9240
Fax: (650) 736-0234

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Re: ObjectJ

vischer
Hello Francie,

let me make just a few statements about ObjectJ:
- it is advisable that you have a basic knowledge of ImageJ before studying the behavior of ObjectJ. I.e. a newbie first should try if ImageJ with its excellent documentation can solve the problem.

- Non-destructive techniques in ImageJ have been considerably enhanced in the last few years: you can store rois in the roi manager, you can give them different colors and names, you can associate them to stack slices, and store them as a set of rois or as part of a tiff file. An additional technique are non-destructive overlays, that can communicate with the roi manager.

- ObjectJ comes to its right when you have hierarchical structures of markers that need to be kept together in composite objects, when you need back-and-forth navigation between results and markers, when you want to conditionally qualify a subset of your marked objects with direct update of the ObjectJ results table and get plots of these subsets.

- ObjectJ  integrates all relevant information (except the images) in a single project file that can be double-clicked. You don't need to use individual files for macros, results, rois nor remember their context (good when you want to resume work after a few months). Also, we avoid external spreadsheet programs (Excel) as much as possible, as the internal results sheet has full macro access without loosing the link to the marked images.

- Back to your question: Possibly you can do your analysis with ImageJ by drawing a roi manually, and use that roi to analyze particles (which only counts particles inside that roi).  But I would need some more explanation about the project.

best regards, Norbert
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