I am capturing fluorescent microscopy images of a developmental process with a high degree of variability. I need to compile these images into a "gallery" so that I can see many/all images at once to look for possible phenotypic differences between conditions, which then I can measure through FIJI. The most basic way I can do this is by arranging the images in a Powerpoint, but this method feels manual and has some limitations (explained below). I am hoping someone may know of a better way to compile image data for investigation/curation, maybe through FIJI, R, or a different dedicated program.
Limitations of Powerpoint:
1. Cannot track sample group or ID: When you upload an image into Powerpoint, there is no way to check its filename. So I am forced to upload one image at a time (and make a text box noting condition and ID), which is slow and unideal for batch processing images.
2. Re-formatting and arranging is manual: Re-sizing, cropping, and positioning images on Powerpoint is very manual and there is no record of changes (so making scale bars is hard). The effort compounded when the need arises to re-size or re-position the images later in the process (see #3).
3. Cannot re-order images dynamically based on values: Because the process I am studying is highly variable, it is necessary to compare images at the same percentile between conditions. Thus, I would like to re-order the images by measured values (so that I can compare min to min, mid to mid, max to max, etc.). This is also useful for selecting representative images for presentations/papers.
4. Interactive/Shiny Graph: To further aid in comparing images based on values, it would be nice to have an interactive/shiny scatterplot of the measured values such that when you hover over/select an image the corresponding datapoint in marked in the graph.
Partial Solutions:
A. Keynote: Solves #1 because uploaded images retain the filename information. However, the file format is limited to Macs which limits data sharing.
B. QuickFigures: This FIJI plugin solves #1 and #2, but it is still clunky to use and cannot re-order images.
C. Image Data Explorer: This R package or browser program solves #4 but can only view one image at a time. It also has the advantage of easy annotation of the images by entering values into the corresponding data spreadsheet/dataframe.
Does anyone know of a way/program that solves any of these limitations? Or does anyone have a different way of compiling image data?
Use python libraries such as Pandas and Matplotlib they help you load and manipulate image data.
Hello Nathan,
It may not be easy, but possible. You can rename files according to the parameters (or calculated values), not manually, in Matlab and Python. Also, you can merge labels into them. You can arrange them in adobe illustrator instead of PowerPoint. There may be better ways, but that comes to mind if I have the same issue.
Good luck!
Grisha
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