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What you should know before using Athena for Zebrafish software:

Image formats

Athena supports loading a broad range of image formats either with or without the associated Metadata.  Images must be either 8-bit or 16-bit grayscale images, as RGB color images are not supported.

Without metadata, supported image formats are *.tif, *.tiff, *.png, *.bmp, *.jpg, *.jpeg.  For these formats, users can manually define pixel size and the software can identify associated color channels present in separate image files.  To group the color channels together, identifying text in the file name of each image should be present e.g., Brightfield_01.tif,  Green_01.tif, Red_01.tif.  Multi-page *.tif image stacks are accepted when each page corresponds either to a Z- or T-stack (time-lapse).  Each Z- or T-slice is analyzed separately and 3D rendering is not supported.

When loading OME-TIFF and proprietary formats (*.czi, *.nd2, etc), Athena can automatically extract the following associated metadata:

1. Dimensions of each image: well, in well field, wavelength, time index, Z-stack index. 
2. Pixel size
3. Plate info
4. Objective

Image characteristics 

Athena for Zebrafish has three requirements to visualize zebrafish embryos or larvae visualized in a micrograph image:

1. The zebrafish animal must be imaged using transmitted light for contour and anatomy detection.  Whole-body fluorescence images are not supported.
2. The transmitted light channel must have a bright (white) background.  Best results are obtained for zebrafish imaged with standard brightfield illumination rather than contrast enhanced transmitted light methodologies (i.e. phase contrast, DIC).  
3. The whole animal must be visible within the image, from head to tail.  Images visualizing only specific regions, such as the heart or tailfin, are not yet supported.

Computer Requirements

• Minimum 8GB ram, preferable 16GB.
• At least 2 cores, preferable 8.
• Monitor screen– To ensure proper software visibility, screen resolution should be set to at least 1920 x 1080 and the text scaling should be set to 100%.