bodenmillergroup / cytoviewer Goto Github PK

By default pixel-wise interpolation is performed. To visualize the raw data, it needs to be turned off.

It would be great to improve the use of svgPanZoom in a way that user input does not change the zoom position of the image (i.e., when zoomed into a single-cell, we can still adjust bcg parameters or marker selection and do not need to zoom in again). Will (most likely) need some Java-Script experience.

Potentially helpful issues/ideas:
timelyportfolio/svgPanZoom#7
https://stackoverflow.com/questions/39817784/r-svgpanzoom-customize-size-and-add-locator?noredirect=1#comment66926839_39817784

Great work! I use cytoviewer for MALDI-images with larger pixel sizes, e.g. 5, 20 or 50um. Is it be possible to implement a feature where I can input a custom and the scale bar value is adjusted? Would be great to have my scale bar in microns rather than pixels. Thanks devs!

Feedback from the Bioc image analysis meeting

Hi @lassedochreden

here are a couple of things that need to be done before Bioc submission:

• Write the vignette
• Expand the cytoviewer man page on what the app is doing when providing different inputs
• Write simple unit tests
• Write validity checks

Great work! I cannot imagine how people in the lab would love this app.

Is it possible to add the feature of creating CytoImageList objects in the app? So that the image, mask, and object can be loaded by selecting folders in the app.

This can easily be done by applying the EBImage::gblur function before plotting.