You can work with grayscale image (with only 1 channel). Basically,what you do is to use /example/imagenet/create_imagenet.sh to create your lmdb / leveldm .mdb files from all your images. But in that script, you need to add --gray option, i.e.,
GLOG_logtostderr=1 $TOOLS/convert_imageset \
--resize_height=$RESIZE_HEIGHT \
--resize_width=$RESIZE_WIDTH \
--shuffle \
--gray \
$VAL_DATA_ROOT \
$DATA/val.txt \
$EXAMPLE/ilsvrc12_val_lmdb
Then, your input can be grayscale image and it should properly.
GLOG_logtostderr=1 $TOOLS/convert_imageset \
--resize_height=$RESIZE_HEIGHT \
--resize_width=$RESIZE_WIDTH \
--shuffle \
--gray \
$TRAIN_DATA_ROOT \
$DATA/train_labeling_3d_axial_z_axis_length_5.txt \
$EXAMPLE/tumor_train_lmdb_3d_axial_z_axis_length_5