I have taken pictures under a microscope using Olympus STREAM software and saved it as .TIFF format. I am having issues getting ImageJ/Bio-Formats from properly reading the spatial calibration data from the .TIFF file.
ImageJ (FIJI) and Bio-Formats is unable to correctly read spatial calibration data from pictures taken under a microscope using Olympus Stream software. The pictures are saved in .TIFF format.
- I tried opening the .TIFF image file using SCIFIO enabled by going to Edit >> Options > ImageJ2.
- I tried using Bio-Formats Importers from Plugins >> Bio-Formats, which also did NOT solve the issue.
In both methods, it seems the spatial calibration data (pixel size and unit type) imported is incorrect. You can also confirm this by looking a the sample pictures I have uploaded.
sample-picture-from-olympus-stream.zip (10.8 MB)
I have attached sample images which include:
- a .TIFF file, 2)
- a .JPG file which contains a scale bar which was embedded by Olumpus STREAM
- a .txt file which contains image properties (metadata) which is outputted by Olympus STREAM.
The .JPG file which has a scale bar scan be used as reference to confirm that when ImageJ/FIJI reads the .TIFF, the imported spatial calibration data is incorrect.
For example, a picture was taken at 10x magnification. Olympus STREAM reports the pixel size of 516.2nm/pixel. However, when the image is opened in ImageJ using Bio-Formats import, the resulting spatial calibration data shows pixel size of 352.7778 pixel/pixel. Therefore, ImageJ/Bio-Formats incorrectly reads the pixel size and the units.
This link contains additional sample TIFF pictures taken using Olympus STREAM: https://app.box.com/s/5pulk5qh75f9zu7eao966w0yxnrvh6rh
It would be great if the dev team can bring support for reading correct spatial calibration metadata from .TIFF pictures taken using OLYMPUS Stream.