Drawing C. elegans germline in Tikz
There are two kinds of patterns: inherently coloured ones and colourless ones. This pattern defined as 'form only'. It isn't intended to take a colour in the definition, which is assumed to be colourless. Instead, use pattern color to set the colour when using the pattern.
\documentclass[border=10pt,11pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{patterns}
\definecolor{dapi}{RGB}{0,170,255}
\def\hexagonsize{0.2cm}
\pgfdeclarepatternformonly % hexagons pattern definition
{hexagons}% name
{\pgfpointorigin}% lower left
{\pgfpoint{3*\hexagonsize}{0.866025*2*\hexagonsize}}% upper right
{\pgfpoint{3*\hexagonsize}{0.866025*2*\hexagonsize}}% tile size
{% shape description
\pgfsetlinewidth{0.4pt}
\pgftransformshift{\pgfpoint{0mm}{0.866025*\hexagonsize}}
\pgfpathmoveto{\pgfpoint{0mm}{0mm}}
\pgfpathlineto{\pgfpoint{0.5*\hexagonsize}{0mm}}
\pgfpathlineto{\pgfpoint{\hexagonsize}{-0.866025*\hexagonsize}}
\pgfpathlineto{\pgfpoint{2*\hexagonsize}{-0.866025*\hexagonsize}}
\pgfpathlineto{\pgfpoint{2.5*\hexagonsize}{0mm}}
\pgfpathlineto{\pgfpoint{3*\hexagonsize+0.2mm}{0mm}}
\pgfpathmoveto{\pgfpoint{0.5*\hexagonsize}{0mm}}
\pgfpathlineto{\pgfpoint{\hexagonsize}{0.866025*\hexagonsize}}
\pgfpathlineto{\pgfpoint{2*\hexagonsize}{0.866025*\hexagonsize}}
\pgfpathlineto{\pgfpoint{2.5*\hexagonsize}{0mm}}
\pgfusepath{stroke}
\pgfsetfillcolor{dapi} % setting up fill color, doesn't work with any color other than shades of gray like "gray!30"
\pgfpathcircle{\pgfpoint{1.5*\hexagonsize}{0mm}}{0.5*\hexagonsize} % adding filled circles in hexagons
\pgfpathcircle{\pgfpoint{0mm}{0.866025*\hexagonsize}}{0.5*\hexagonsize}
\pgfpathcircle{\pgfpoint{0mm}{-0.866025*\hexagonsize}}{0.5*\hexagonsize}
\pgfpathcircle{\pgfpoint{3*\hexagonsize}{0.866025*\hexagonsize}}{0.5*\hexagonsize}
\pgfpathcircle{\pgfpoint{3*\hexagonsize}{-0.866025*\hexagonsize}}{0.5*\hexagonsize}
\pgfusepath{fill}
}
\begin{document}
\begin{tikzpicture}
\path
[fill]
[pattern=hexagons, pattern color=dapi]
(16,0) -- (4,0) to [out = 180, in = 270] (1,0.95) to [out = 90, in = 180] (4,1.9) -- (16,1.9) -- cycle;
\fill[green!35] (4,0) to [out = 180, in = 270] (0.5,0.95) to [out = 90, in = 180] (4,1.9) to
[out = 180, in = 90](1,0.95) to [out = 270, in = 180] (4,0);
\fill [blue!50](0.75,1) circle [x radius=3mm, y radius=1.5mm, rotate=60];
\end{tikzpicture}
\end{document}
However, if you need different nuclei, then you cannot do that with a pattern. You could, theoretically, draw the hexagons as a pattern and then add the nuclei separately. However, that would probably be rather error-prone, even if slightly faster in terms of compilation time. It is probably easier and more robust to draw the nuclei along with the hexagonal cell containing it. That way, you can introduce as much variety as you like.
For example,
\documentclass[border=10pt,11pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{shapes.geometric}
\definecolor{dapi}{RGB}{0,170,255}
\begin{document}
\begin{tikzpicture}
[
hexa/.style={draw=dapi, minimum size=\hdim, inner sep=0pt, regular polygon, regular polygon sides=6, anchor=center},
nucleus/.style={fill, minimum size=.35*\hdim, inner sep=0pt, circle, anchor=center},
]
\begin{scope}
\clip (16,0) coordinate (d) -- (4,0) coordinate (a) to [out = 180, in = 270] (1,0.95) coordinate (b) to [out = 90, in = 180] (4,1.9) coordinate (c) -- (d |- c) -- cycle (b |- c) coordinate (h0-0);
\newdimen\hdim
\newdimen\odim
\hdim=3mm
\pgfmathsetlength\odim{0.866025*\hdim}
\foreach \j [remember=\j as \jlast (initially 0)] in {1,...,70}
\foreach \i [remember=\i as \ilast (initially 0) ] in {1,...,8}
{
\ifodd\j\def\tempa{30}\else\def\tempa{-30}\fi
\ifnum\j<21\def\tempb{green}\else\def\tempb{red}\fi
\ifnum\j=19\ifnum\i=3\def\tempb{red}\fi\ifnum\i=7\def\tempb{red}\fi\fi
\ifnum\j=20\ifnum\i=1\def\tempb{red}\fi\ifnum\i=5\def\tempb{red}\fi\ifnum\i=8\def\tempb{red}\fi\fi
\ifnum\j=22\ifnum\i=4\def\tempb{green}\fi\fi
\ifnum\j=24\ifnum\i=7\def\tempb{green}\fi\fi
\ifnum\j=25\ifnum\i=6\def\tempb{green}\fi\fi
\ifnum\j=24\ifnum\i=2\def\tempb{green}\fi\fi
\ifnum\j=26\ifnum\i=3\def\tempb{green}\fi\fi
\ifnum\j=21\ifnum\i=5\def\tempb{green}\fi\fi
\ifnum\i=1
\ifnum\j=1\path (h0-0) node (h\j-\i) [hexa] {} node [nucleus, \tempb] {};
\else\path ([shift=(\tempa:\odim)]h\jlast-1) node (h\j-\i) [hexa] {} node [nucleus, \tempb] {};
\fi
\else\path ([yshift=-\odim]h\j-\ilast) node (h\j-\i) [hexa] {} node [nucleus, \tempb] {};
\fi
};
\end{scope}
\fill[green!35] (a) to [out = 180, in = 270] (0.5,0.95) to [out = 90, in = 180] (c) to
[out = 180, in = 90] (b) to [out = 270, in = 180] (a);
\fill [blue!50] (0.75,1) circle [x radius=3mm, y radius=1.5mm, rotate=60];
\end{tikzpicture}
\end{document}
Here is my final picture based on the answer from @cfr with little changes to include crescent nuclei, with random rotations, after meiotic entry. Might be useful for some.
The codes are,
\documentclass[border=10pt,11pt]{article}
\usepackage{tikz}
\usetikzlibrary{shapes.geometric}
\definecolor{dapi}{RGB}{0,170,255}
\begin{document}
\begin{tikzpicture}
[
hexa/.style={draw=dapi, minimum size=\hdim, inner sep=0pt, regular polygon, regular polygon sides=6, anchor=center},
nucleus/.style={fill, minimum size=.5*\hdim, inner sep=0pt, circle, anchor=center},
crescent/.style={fill = white, minimum size=.35*\hdim, inner sep=0pt, circle, anchor=south}
]
\begin{scope}
\clip (16,0) coordinate (d) -- (4,0) coordinate (a) to [out = 180, in = 270] (1,0.95) coordinate (b) to [out = 90, in = 180] (4,1.9) coordinate (c) -- (d |- c) -- cycle (b |- c) coordinate (h0-0);
\newdimen\hdim
\newdimen\odim
\hdim=3.5mm
\pgfmathsetlength\odim{0.866025*\hdim}
\def\tempc{0}
\foreach \j [remember=\j as \jlast (initially 0)] in {1,...,70}
\foreach \i [remember=\i as \ilast (initially 0) ] in {1,...,8}
\pgfmathsetseed{\j+\i} % for reproducibility
\pgfmathrandominteger{\k}{1}{360} % k is (randomly) defind to rotate crescent nuclei
{
\ifodd\j\def\tempa{30}\else\def\tempa{-30}\fi
\ifnum\j<21\def\tempb{green}\else\def\tempb{red}\fi
\ifnum\j=19\ifnum\i=3\def\tempb{red}\fi\fi % tempb - to add red nuclei in progenitor zone and green nuclei in leptotene/zygotene
\ifnum\j=20\ifnum\i=5\def\tempb{red}\fi\fi
\ifnum\j=21\ifnum\i=5\def\tempb{green}\fi\fi
\ifnum\j=22\ifnum\i=4\def\tempb{green}\fi\fi
\ifnum\j=24\ifnum\i=7\def\tempb{green}\fi\fi
\ifnum\j=25\ifnum\i=6\def\tempb{green}\fi\fi
\ifnum\j=24\ifnum\i=2\def\tempb{green}\fi\fi
\ifnum\j=26\ifnum\i=3\def\tempb{green}\fi\fi
\ifnum\j=21\ifnum\i=4\def\tempc{1}\fi\fi % tempc for adding crescent shaped nuclei in laeptotene/zygotene region
\ifnum\j=21\ifnum\i=6\def\tempc{1}\fi\fi
\ifnum\j=22\ifnum\i=2\def\tempc{1}\fi\fi
\ifnum\j=22\ifnum\i=5\def\tempc{1}\fi\fi
\ifnum\j=22\ifnum\i=7\def\tempc{1}\fi\fi
\ifnum\j=23\ifnum\i=2\def\tempc{1}\fi\fi
\ifnum\j=23\ifnum\i=6\def\tempc{1}\fi\fi
\ifnum\j=23\ifnum\i=7\def\tempc{1}\fi\fi
\ifnum\j=24\ifnum\i=1\def\tempc{1}\fi\fi
\ifnum\j=24\ifnum\i=4\def\tempc{1}\fi\fi
\ifnum\j=25\ifnum\i=3\def\tempc{1}\fi\fi
\ifnum\j=25\ifnum\i=4\def\tempc{1}\fi\fi
\ifnum\j=25\ifnum\i=7\def\tempc{1}\fi\fi
\ifnum\j=26\ifnum\i=1\def\tempc{1}\fi\fi
\ifnum\j=26\ifnum\i=5\def\tempc{1}\fi\fi
\ifnum\j=27\ifnum\i=3\def\tempc{1}\fi\fi
\ifnum\j=27\ifnum\i=5\def\tempc{1}\fi\fi
\ifnum\j=28\ifnum\i=2\def\tempc{1}\fi\fi
\ifnum\j=28\ifnum\i=5\def\tempc{1}\fi\fi
\ifnum\j=28\ifnum\i=6\def\tempc{1}\fi\fi
\ifnum\j=29\ifnum\i=5\def\tempc{1}\fi\fi
\ifnum\j=31\ifnum\i=2\def\tempc{1}\fi\fi
\ifnum\i=1
\ifnum\j=1\path (h0-0) node (h\j-\i) [hexa] {} node [nucleus, \tempb] {} node [crescent, rotate=\k,opacity = \tempc] {};
\else\path ([shift=(\tempa:\odim)]h\jlast-1) node (h\j-\i) [hexa] {} node [nucleus, \tempb] {} node [crescent, rotate=\k,opacity = \tempc] {};
\fi
\else\path ([yshift=-\odim]h\j-\ilast) node (h\j-\i) [hexa] {} node [nucleus, \tempb] {}
node [crescent, rotate=\k,opacity = \tempc] {};
\fi
};
\end{scope}
\fill[pink!45] (a) to [out = 180, in = 270] (0.5,0.95) to [out = 90, in = 180] (c) to
[out = 180, in = 90] (b) to [out = 270, in = 180] (a);
\fill [dapi] (0.75,1) circle [x radius=3mm, y radius=1.5mm, rotate=60];
\node[above, rotate=90] (DTC) at (0.5,0.95) {DTC};
\node[below, rotate = -30] (ME) at (6.4,0) {ME};
\draw[dashed, ultra thick, color = blue] (6.13,1.9) -- (6.13,0);
\node[above] (pz) at (4,1.9) {Progenitor Zone};
\node[above] (lz) at (7,1.9) [align=left]{Leptotene/ \\Zygotene};
\node[above] (pachytene) at (10,1.9) {Pachytene};
\end{tikzpicture}
\end{document}
Thanks again to @cfr and @PaulGaborit.