Fig. 7

Block diagram of the image generation pipeline. The cell spherocylinder image is first morphed using the roll function and multiplied by \(I_c\), the empirical cell intensity. To this image is added the trench OPL image, which is multiplied by \(I_t\), the empirical trench intensity. Finally, the media image is added with those pixels being multiplied by \(I_m\), the empirical media intensity. These steps are described in detail in Additional file 1, Section 3. The PSF, which has been altered by Gaussian apodisation, and simulated defocus is then convolved over the image. The precise implementation of the PSF and its modifications are described in Additional file 1, Section 4. The camera-modelled shot noise and read noise are then added to the image (implementation details in Additional file 1, Section 6 [39], with optional Fourier and intensity matching occurring after (Additional file 1, Section 7, [40]). Combined, this produces a synthetic image realistic enough to train highly accurate models for image segmentation of real data