diff --git a/image_ref/img_ref_aligned/Citrobacter amalonaticus.npy b/image_ref/img_ref_aligned/Citrobacter amalonaticus.npy
new file mode 100644
index 0000000000000000000000000000000000000000..3163b29ec21d702fdfe4b94cdaec5f39e40b9b2a
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter amalonaticus.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter amalonaticus.png b/image_ref/img_ref_aligned/Citrobacter amalonaticus.png
new file mode 100644
index 0000000000000000000000000000000000000000..1378822235c3561eca25a3b156a66795346b4306
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter amalonaticus.png differ
diff --git a/image_ref/img_ref_aligned/Citrobacter braakii.npy b/image_ref/img_ref_aligned/Citrobacter braakii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..ad0ee948a960fed9c23206febb19ee7ce3f429c6
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter braakii.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter braakii.png b/image_ref/img_ref_aligned/Citrobacter braakii.png
new file mode 100644
index 0000000000000000000000000000000000000000..f72465175e7642142605c3320e8d743f18bdf7d5
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter braakii.png differ
diff --git a/image_ref/img_ref_aligned/Citrobacter cronae.npy b/image_ref/img_ref_aligned/Citrobacter cronae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..ff788c3ae15ef65130fa391823485266f005203c
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter cronae.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter cronae.png b/image_ref/img_ref_aligned/Citrobacter cronae.png
new file mode 100644
index 0000000000000000000000000000000000000000..1af52caa3b553408085f184ffca81642a43deeb4
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter cronae.png differ
diff --git a/image_ref/img_ref_aligned/Citrobacter farmeri.npy b/image_ref/img_ref_aligned/Citrobacter farmeri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..492554bce930b13efc8231c5aea7ad634074a272
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter farmeri.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter farmeri.png b/image_ref/img_ref_aligned/Citrobacter farmeri.png
new file mode 100644
index 0000000000000000000000000000000000000000..30b66f60e4d457a55f441dc4ffd71b8838e3f16f
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter farmeri.png differ
diff --git a/image_ref/img_ref_aligned/Citrobacter freundii.npy b/image_ref/img_ref_aligned/Citrobacter freundii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7a3621933e36ff69efb617eee632937ee3ed6b53
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter freundii.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter freundii.png b/image_ref/img_ref_aligned/Citrobacter freundii.png
new file mode 100644
index 0000000000000000000000000000000000000000..a365a5cda5b3d486936aae2d8886bcc4cb87af3b
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter freundii.png differ
diff --git a/image_ref/img_ref_aligned/Citrobacter koseri.npy b/image_ref/img_ref_aligned/Citrobacter koseri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..3695fa2d26050ff40031e9cc8dc129e322e7c9e5
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter koseri.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter koseri.png b/image_ref/img_ref_aligned/Citrobacter koseri.png
new file mode 100644
index 0000000000000000000000000000000000000000..b676641c47d92d6cf38add3f6afc0a60b7da9610
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter koseri.png differ
diff --git a/image_ref/img_ref_aligned/Citrobacter portucalensis.npy b/image_ref/img_ref_aligned/Citrobacter portucalensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..3eda84964425df2ac536f675f5065a71feff117a
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter portucalensis.npy differ
diff --git a/image_ref/img_ref_aligned/Citrobacter portucalensis.png b/image_ref/img_ref_aligned/Citrobacter portucalensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..a899732dd60695052db284757feeeed79ba7a274
Binary files /dev/null and b/image_ref/img_ref_aligned/Citrobacter portucalensis.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter asburiae.npy b/image_ref/img_ref_aligned/Enterobacter asburiae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..c09d2952df172258ecd209ee3fd8712c177c1737
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter asburiae.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter asburiae.png b/image_ref/img_ref_aligned/Enterobacter asburiae.png
new file mode 100644
index 0000000000000000000000000000000000000000..4d44e2e00cf7394f9d1a5b98921c9895dff4dd34
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter asburiae.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter bugandensis.npy b/image_ref/img_ref_aligned/Enterobacter bugandensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..d820220f0b561fb1867c52ecb75944c9992154bc
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter bugandensis.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter bugandensis.png b/image_ref/img_ref_aligned/Enterobacter bugandensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..fe91e2d4fce49afb475811981c4372d9a3f2e8d2
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter bugandensis.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter chengduensis.npy b/image_ref/img_ref_aligned/Enterobacter chengduensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..3e40e9d4cb05fc0579e3a91f20e73d996118d14e
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter chengduensis.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter chengduensis.png b/image_ref/img_ref_aligned/Enterobacter chengduensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..3f9454fa964c0a083d9b0e4b737c8cfaa4e94896
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter chengduensis.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter cloacae.npy b/image_ref/img_ref_aligned/Enterobacter cloacae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..430b99d1adf42968232d5ae29407e5c015d676f2
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter cloacae.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter cloacae.png b/image_ref/img_ref_aligned/Enterobacter cloacae.png
new file mode 100644
index 0000000000000000000000000000000000000000..faeebeebccc5779ee19928885e80bacdefcdeb45
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter cloacae.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter hormaechei.npy b/image_ref/img_ref_aligned/Enterobacter hormaechei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e5e8f76a660df6c7da2e823c76564d1ee2014ac6
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter hormaechei.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter hormaechei.png b/image_ref/img_ref_aligned/Enterobacter hormaechei.png
new file mode 100644
index 0000000000000000000000000000000000000000..29c2f25dd7e88597fc23d3239fb0e138cfa82889
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter hormaechei.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter kobei.npy b/image_ref/img_ref_aligned/Enterobacter kobei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..3ea75034a206805fec4144ab2f188696863067f1
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter kobei.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter kobei.png b/image_ref/img_ref_aligned/Enterobacter kobei.png
new file mode 100644
index 0000000000000000000000000000000000000000..c0109770ab7d5e875977b0abc0f79d27d3d9ec7f
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter kobei.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter ludwigii.npy b/image_ref/img_ref_aligned/Enterobacter ludwigii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..945de83a3c1caa3fc51bab5fc02d87d3c02d455c
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter ludwigii.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter ludwigii.png b/image_ref/img_ref_aligned/Enterobacter ludwigii.png
new file mode 100644
index 0000000000000000000000000000000000000000..9b69094314294a81f729a8962b733c73ec29ea26
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter ludwigii.png differ
diff --git a/image_ref/img_ref_aligned/Enterobacter roggenkampii.npy b/image_ref/img_ref_aligned/Enterobacter roggenkampii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..bf1322eece5e7813bbe108c617f7dcf7cf37160d
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter roggenkampii.npy differ
diff --git a/image_ref/img_ref_aligned/Enterobacter roggenkampii.png b/image_ref/img_ref_aligned/Enterobacter roggenkampii.png
new file mode 100644
index 0000000000000000000000000000000000000000..5cf88a70d7f8a5ac75c23ad0b13b6eb3e7a144cc
Binary files /dev/null and b/image_ref/img_ref_aligned/Enterobacter roggenkampii.png differ
diff --git a/image_ref/img_ref_aligned/Escherichia coli.npy b/image_ref/img_ref_aligned/Escherichia coli.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e17b9ecb323197dbf9d144e0c4fef05c3b85ee37
Binary files /dev/null and b/image_ref/img_ref_aligned/Escherichia coli.npy differ
diff --git a/image_ref/img_ref_aligned/Escherichia coli.png b/image_ref/img_ref_aligned/Escherichia coli.png
new file mode 100644
index 0000000000000000000000000000000000000000..8c91a7644a6a2fa3ba43141d6b919845e4b5b484
Binary files /dev/null and b/image_ref/img_ref_aligned/Escherichia coli.png differ
diff --git a/image_ref/img_ref_aligned/Hafnia alvei.npy b/image_ref/img_ref_aligned/Hafnia alvei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..70bed6af52e557bc7498cc9ff42448ab766130fb
Binary files /dev/null and b/image_ref/img_ref_aligned/Hafnia alvei.npy differ
diff --git a/image_ref/img_ref_aligned/Hafnia alvei.png b/image_ref/img_ref_aligned/Hafnia alvei.png
new file mode 100644
index 0000000000000000000000000000000000000000..1ca7b1cd4db183cf5295b966cefb6234af0f69b5
Binary files /dev/null and b/image_ref/img_ref_aligned/Hafnia alvei.png differ
diff --git a/image_ref/img_ref_aligned/Hafnia paralvei.npy b/image_ref/img_ref_aligned/Hafnia paralvei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..080d9f6d64a46cc70209e22838f94995fccaab9e
Binary files /dev/null and b/image_ref/img_ref_aligned/Hafnia paralvei.npy differ
diff --git a/image_ref/img_ref_aligned/Hafnia paralvei.png b/image_ref/img_ref_aligned/Hafnia paralvei.png
new file mode 100644
index 0000000000000000000000000000000000000000..8890ec7f152e26223e06a76463cb3c565959ddbb
Binary files /dev/null and b/image_ref/img_ref_aligned/Hafnia paralvei.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella aerogenes.npy b/image_ref/img_ref_aligned/Klebsiella aerogenes.npy
new file mode 100644
index 0000000000000000000000000000000000000000..d87abb2a88861a4275ed3eda32ff4b2fcb13d8f4
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella aerogenes.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella aerogenes.png b/image_ref/img_ref_aligned/Klebsiella aerogenes.png
new file mode 100644
index 0000000000000000000000000000000000000000..89de6e9d8838dba01fde94fa4cd157319562f71a
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella aerogenes.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella grimontii.npy b/image_ref/img_ref_aligned/Klebsiella grimontii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..547b9137b1cee99067de53a34030039baf348803
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella grimontii.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella grimontii.png b/image_ref/img_ref_aligned/Klebsiella grimontii.png
new file mode 100644
index 0000000000000000000000000000000000000000..73c2def6f97d70682ba40aa77468af8f73597d70
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella grimontii.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella michiganensis.npy b/image_ref/img_ref_aligned/Klebsiella michiganensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..a7550a78fa9d9b5b4ac60370a6ff9829e3382ba5
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella michiganensis.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella michiganensis.png b/image_ref/img_ref_aligned/Klebsiella michiganensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..2564761eb956da779d89a6ef7825f3749584364c
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella michiganensis.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella oxytoca.npy b/image_ref/img_ref_aligned/Klebsiella oxytoca.npy
new file mode 100644
index 0000000000000000000000000000000000000000..283425f918058975d4838b63ffbfc57ca5003da5
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella oxytoca.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella oxytoca.png b/image_ref/img_ref_aligned/Klebsiella oxytoca.png
new file mode 100644
index 0000000000000000000000000000000000000000..d72fa91cf3c2e34a7314778a4c00836df46abd64
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella oxytoca.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella pneumoniae.npy b/image_ref/img_ref_aligned/Klebsiella pneumoniae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..cc938df81c4b7db9f05c591af595c443488a01d8
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella pneumoniae.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella pneumoniae.png b/image_ref/img_ref_aligned/Klebsiella pneumoniae.png
new file mode 100644
index 0000000000000000000000000000000000000000..b26a85cf76aa753d07a1408c0b4453d7a0b8edb4
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella pneumoniae.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella quasipneumoniae.npy b/image_ref/img_ref_aligned/Klebsiella quasipneumoniae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2123c0a8c583cae672c0d67aa8160dd70ceda064
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella quasipneumoniae.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella quasipneumoniae.png b/image_ref/img_ref_aligned/Klebsiella quasipneumoniae.png
new file mode 100644
index 0000000000000000000000000000000000000000..c21a81bf430efaf4765c4f04a493357b28b79108
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella quasipneumoniae.png differ
diff --git a/image_ref/img_ref_aligned/Klebsiella variicola.npy b/image_ref/img_ref_aligned/Klebsiella variicola.npy
new file mode 100644
index 0000000000000000000000000000000000000000..9d9f3e4c2c6933e11142d590206422451cabce08
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella variicola.npy differ
diff --git a/image_ref/img_ref_aligned/Klebsiella variicola.png b/image_ref/img_ref_aligned/Klebsiella variicola.png
new file mode 100644
index 0000000000000000000000000000000000000000..31738930b191047e41463b5bbcad0fc5072530bf
Binary files /dev/null and b/image_ref/img_ref_aligned/Klebsiella variicola.png differ
diff --git a/image_ref/img_ref_aligned/Morganella morganii.npy b/image_ref/img_ref_aligned/Morganella morganii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..a22b72fbdad65e6bd5c9737a0f3ae6729184dfc8
Binary files /dev/null and b/image_ref/img_ref_aligned/Morganella morganii.npy differ
diff --git a/image_ref/img_ref_aligned/Morganella morganii.png b/image_ref/img_ref_aligned/Morganella morganii.png
new file mode 100644
index 0000000000000000000000000000000000000000..4d309be13b1285bffb3c6e2ef0b7a81e5fcf8abb
Binary files /dev/null and b/image_ref/img_ref_aligned/Morganella morganii.png differ
diff --git a/image_ref/img_ref_aligned/Pantoea agglomerans.npy b/image_ref/img_ref_aligned/Pantoea agglomerans.npy
new file mode 100644
index 0000000000000000000000000000000000000000..038c1c94ff42d64ba3b6113e98cdd107e3dfe0d7
Binary files /dev/null and b/image_ref/img_ref_aligned/Pantoea agglomerans.npy differ
diff --git a/image_ref/img_ref_aligned/Pantoea agglomerans.png b/image_ref/img_ref_aligned/Pantoea agglomerans.png
new file mode 100644
index 0000000000000000000000000000000000000000..908eb9b3da6dcd25af0d35bd354215a345334058
Binary files /dev/null and b/image_ref/img_ref_aligned/Pantoea agglomerans.png differ
diff --git a/image_ref/img_ref_aligned/Pantoea septica.npy b/image_ref/img_ref_aligned/Pantoea septica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..fc2136d94b44bdac68e3983aceb55087d1f978f7
Binary files /dev/null and b/image_ref/img_ref_aligned/Pantoea septica.npy differ
diff --git a/image_ref/img_ref_aligned/Pantoea septica.png b/image_ref/img_ref_aligned/Pantoea septica.png
new file mode 100644
index 0000000000000000000000000000000000000000..54f603f12fb342833e3f2fbaaeaafda2238b4c8c
Binary files /dev/null and b/image_ref/img_ref_aligned/Pantoea septica.png differ
diff --git a/image_ref/img_ref_aligned/Proteus columbae.npy b/image_ref/img_ref_aligned/Proteus columbae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..eefb5ad1a9e81f5322de05ab1e5dfc23b4f6e5a5
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus columbae.npy differ
diff --git a/image_ref/img_ref_aligned/Proteus columbae.png b/image_ref/img_ref_aligned/Proteus columbae.png
new file mode 100644
index 0000000000000000000000000000000000000000..78d84e62cc3c05aa7b3c6b0b060fc8be47c37e4d
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus columbae.png differ
diff --git a/image_ref/img_ref_aligned/Proteus mirabilis.npy b/image_ref/img_ref_aligned/Proteus mirabilis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..cc61ca3c54def070af67c38ce3e8f3ae65056f68
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus mirabilis.npy differ
diff --git a/image_ref/img_ref_aligned/Proteus mirabilis.png b/image_ref/img_ref_aligned/Proteus mirabilis.png
new file mode 100644
index 0000000000000000000000000000000000000000..836e2e5da1dc8693f424c3f8c062f1f6980a4b7b
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus mirabilis.png differ
diff --git a/image_ref/img_ref_aligned/Proteus penneri.npy b/image_ref/img_ref_aligned/Proteus penneri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..b8a5dcfd3a49a6739b34652ead1b2e72c6d3cad7
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus penneri.npy differ
diff --git a/image_ref/img_ref_aligned/Proteus penneri.png b/image_ref/img_ref_aligned/Proteus penneri.png
new file mode 100644
index 0000000000000000000000000000000000000000..5f9cb40bf5de5f6f53128674e85018af0513c53c
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus penneri.png differ
diff --git a/image_ref/img_ref_aligned/Proteus terrae.npy b/image_ref/img_ref_aligned/Proteus terrae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..0b91e465e9512797649546f2fbd72f224a2a6c78
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus terrae.npy differ
diff --git a/image_ref/img_ref_aligned/Proteus terrae.png b/image_ref/img_ref_aligned/Proteus terrae.png
new file mode 100644
index 0000000000000000000000000000000000000000..9fb1564d99fffdc8a5ee3175e88c3e18b2206162
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus terrae.png differ
diff --git a/image_ref/img_ref_aligned/Proteus vulgaris.npy b/image_ref/img_ref_aligned/Proteus vulgaris.npy
new file mode 100644
index 0000000000000000000000000000000000000000..463d5850d1bd6a7ceeb44fa641538d1112bd0938
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus vulgaris.npy differ
diff --git a/image_ref/img_ref_aligned/Proteus vulgaris.png b/image_ref/img_ref_aligned/Proteus vulgaris.png
new file mode 100644
index 0000000000000000000000000000000000000000..c66940435f5d21d40cadf264e1ba9be6941382e7
Binary files /dev/null and b/image_ref/img_ref_aligned/Proteus vulgaris.png differ
diff --git a/image_ref/img_ref_aligned/Providencia rettgeri.npy b/image_ref/img_ref_aligned/Providencia rettgeri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..ec8e2e98cbd7a3080daba2130a09aaf955cad261
Binary files /dev/null and b/image_ref/img_ref_aligned/Providencia rettgeri.npy differ
diff --git a/image_ref/img_ref_aligned/Providencia rettgeri.png b/image_ref/img_ref_aligned/Providencia rettgeri.png
new file mode 100644
index 0000000000000000000000000000000000000000..1e2064ca4fede8d3ce6864fa136ccadbb5360c0e
Binary files /dev/null and b/image_ref/img_ref_aligned/Providencia rettgeri.png differ
diff --git a/image_ref/img_ref_aligned/Providencia stuartii.npy b/image_ref/img_ref_aligned/Providencia stuartii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..0055f069059396175dfe1a148eac5d239eccf8d8
Binary files /dev/null and b/image_ref/img_ref_aligned/Providencia stuartii.npy differ
diff --git a/image_ref/img_ref_aligned/Providencia stuartii.png b/image_ref/img_ref_aligned/Providencia stuartii.png
new file mode 100644
index 0000000000000000000000000000000000000000..e159060c4769a718fce4d1f606d3a52648f34852
Binary files /dev/null and b/image_ref/img_ref_aligned/Providencia stuartii.png differ
diff --git a/image_ref/img_ref_aligned/Raoultella ornithinolytica.npy b/image_ref/img_ref_aligned/Raoultella ornithinolytica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7358c6e77d766f2256197cebdb07df133989c60c
Binary files /dev/null and b/image_ref/img_ref_aligned/Raoultella ornithinolytica.npy differ
diff --git a/image_ref/img_ref_aligned/Raoultella ornithinolytica.png b/image_ref/img_ref_aligned/Raoultella ornithinolytica.png
new file mode 100644
index 0000000000000000000000000000000000000000..a142cb3b84738563b3fccf13cbaebe303d9a95ee
Binary files /dev/null and b/image_ref/img_ref_aligned/Raoultella ornithinolytica.png differ
diff --git a/image_ref/img_ref_aligned/Salmonella enterica.npy b/image_ref/img_ref_aligned/Salmonella enterica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2de58ea3c10f84113393d7d7907a9036714b0a4f
Binary files /dev/null and b/image_ref/img_ref_aligned/Salmonella enterica.npy differ
diff --git a/image_ref/img_ref_aligned/Salmonella enterica.png b/image_ref/img_ref_aligned/Salmonella enterica.png
new file mode 100644
index 0000000000000000000000000000000000000000..f07218c95ff4b53e5e079fce786b746df089325e
Binary files /dev/null and b/image_ref/img_ref_aligned/Salmonella enterica.png differ
diff --git a/image_ref/img_ref_aligned/Serratia marcescens.npy b/image_ref/img_ref_aligned/Serratia marcescens.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e4c77d9894c302d94338dea57669f3067ccc0595
Binary files /dev/null and b/image_ref/img_ref_aligned/Serratia marcescens.npy differ
diff --git a/image_ref/img_ref_aligned/Serratia marcescens.png b/image_ref/img_ref_aligned/Serratia marcescens.png
new file mode 100644
index 0000000000000000000000000000000000000000..d58de857c53bfbbe426333f850b058ed9c7f310d
Binary files /dev/null and b/image_ref/img_ref_aligned/Serratia marcescens.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter amalonaticus.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter amalonaticus.npy
new file mode 100644
index 0000000000000000000000000000000000000000..232ce50c15e05fe3b4edf307e46573588b42d4ee
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter amalonaticus.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter amalonaticus.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter amalonaticus.png
new file mode 100644
index 0000000000000000000000000000000000000000..d6aa42d88f95ab405f25a3f6389dc024b9ebe854
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter amalonaticus.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter braakii.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter braakii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..5922baba2c68d2eaad9c916fcb45c8562de7831d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter braakii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter braakii.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter braakii.png
new file mode 100644
index 0000000000000000000000000000000000000000..532501e42c174f4dacafffd656327452799c7b24
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter braakii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter cronae.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter cronae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..57fa4fd16ae23e1a95c386fe209e6dc3c3731cc9
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter cronae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter cronae.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter cronae.png
new file mode 100644
index 0000000000000000000000000000000000000000..07fd9a6fdd22a8f63adb348574597bf4a2bafe14
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter cronae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter farmeri.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter farmeri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..4208c5c2a84a834700b22e2e31843168abff4b2a
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter farmeri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter farmeri.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter farmeri.png
new file mode 100644
index 0000000000000000000000000000000000000000..79ad51a45f06698230bfcc5c7522ab71705b5b9f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter farmeri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter freundii.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter freundii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..5e40876171e465528de0c9019ea1c44745c440dd
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter freundii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter freundii.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter freundii.png
new file mode 100644
index 0000000000000000000000000000000000000000..e2eb501caec0621b9a460c1e7a4fa2aeb42436cf
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter freundii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter koseri.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter koseri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..610344e2a84de5031b42c8c03164ab160d58428e
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter koseri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter koseri.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter koseri.png
new file mode 100644
index 0000000000000000000000000000000000000000..38a4eb2adbd54c2d2cae4063d672f6b03332ca02
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter koseri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter portucalensis.npy b/image_ref/img_ref_aligned_count_th_10/Citrobacter portucalensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..febb7fab61db84d9e5f7b608b3d07609bff4a25f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter portucalensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Citrobacter portucalensis.png b/image_ref/img_ref_aligned_count_th_10/Citrobacter portucalensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..2f20953047c679b6c245eca75d4f208ae8366728
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Citrobacter portucalensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter asburiae.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter asburiae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..8d51d9c3bd59d36df5f5831510ddc6a8c7705f9e
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter asburiae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter asburiae.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter asburiae.png
new file mode 100644
index 0000000000000000000000000000000000000000..7fc41aa32ffa1099e50db6e243445d27a8f27644
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter asburiae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter bugandensis.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter bugandensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..eae327b9db16e94e4dc68dff17803e24e5d2284d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter bugandensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter bugandensis.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter bugandensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..61971d5936241a962a0eeb27c69b7d06fe2ab33d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter bugandensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter chengduensis.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter chengduensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7a523bc327b3e5811bdfc5878c7bf35230343065
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter chengduensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter chengduensis.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter chengduensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..63ef5f7021480062a74848845aaba689cc995b16
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter chengduensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter cloacae.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter cloacae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..c5a6629ceb6b319783234f0261b1eae316548570
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter cloacae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter cloacae.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter cloacae.png
new file mode 100644
index 0000000000000000000000000000000000000000..3140a49750d646d8e6d1026fde56652327aa7760
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter cloacae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter hormaechei.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter hormaechei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e669b988050a08d2798effeea064f8a9006dd58d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter hormaechei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter hormaechei.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter hormaechei.png
new file mode 100644
index 0000000000000000000000000000000000000000..9d8e77931d15580dff27c3033c80341ded26f5c2
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter hormaechei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter kobei.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter kobei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2406514f65a171b8a971749e756da0a9d3b95832
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter kobei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter kobei.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter kobei.png
new file mode 100644
index 0000000000000000000000000000000000000000..0b76be56414a0b33ecf324242fe4a6db1272d176
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter kobei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter ludwigii.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter ludwigii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..371e95c2cf1b88d90d8f6da738108f7c72fd68ce
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter ludwigii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter ludwigii.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter ludwigii.png
new file mode 100644
index 0000000000000000000000000000000000000000..6b7a054fac8d59504b79ea30f53cb8de10e24759
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter ludwigii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter roggenkampii.npy b/image_ref/img_ref_aligned_count_th_10/Enterobacter roggenkampii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..b67b5524ed66c10cc9d2f0833a351e68b3f850e4
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter roggenkampii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Enterobacter roggenkampii.png b/image_ref/img_ref_aligned_count_th_10/Enterobacter roggenkampii.png
new file mode 100644
index 0000000000000000000000000000000000000000..a110d1c5be0bd3a292a24ac6729688d4121fb200
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Enterobacter roggenkampii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Escherichia coli.npy b/image_ref/img_ref_aligned_count_th_10/Escherichia coli.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7d47b9a6a9c582370a600e12f23a336dbdfca994
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Escherichia coli.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Escherichia coli.png b/image_ref/img_ref_aligned_count_th_10/Escherichia coli.png
new file mode 100644
index 0000000000000000000000000000000000000000..fc3bac8980ee739d4da02e6ce88b5e662a6138e6
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Escherichia coli.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Hafnia alvei.npy b/image_ref/img_ref_aligned_count_th_10/Hafnia alvei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2347b97c9650373803940c8d467f802a6409f4f9
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Hafnia alvei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Hafnia alvei.png b/image_ref/img_ref_aligned_count_th_10/Hafnia alvei.png
new file mode 100644
index 0000000000000000000000000000000000000000..936eac208c4b95dda9b7c3d2f8b40825f61d6ff7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Hafnia alvei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Hafnia paralvei.npy b/image_ref/img_ref_aligned_count_th_10/Hafnia paralvei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7f7a6d04f10120c3629b722033bbb82e9d31a6a6
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Hafnia paralvei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Hafnia paralvei.png b/image_ref/img_ref_aligned_count_th_10/Hafnia paralvei.png
new file mode 100644
index 0000000000000000000000000000000000000000..7966d6f2065765ca6c8ca5882b490a0910169068
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Hafnia paralvei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella aerogenes.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella aerogenes.npy
new file mode 100644
index 0000000000000000000000000000000000000000..0e511452b6833e4d4532fe2b875d239263db7d78
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella aerogenes.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella aerogenes.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella aerogenes.png
new file mode 100644
index 0000000000000000000000000000000000000000..123c089623bb412194b8b698c58028b276b86493
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella aerogenes.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella grimontii.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella grimontii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7e5421996b3bbb993fb30fc51c834177e0d7d073
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella grimontii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella grimontii.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella grimontii.png
new file mode 100644
index 0000000000000000000000000000000000000000..0e18781a33fc3487b8e0c6d2c3e9eebb7c21b26a
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella grimontii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella michiganensis.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella michiganensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..af7b9a673ad582dfb5d9ff738c972a1d9394f24f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella michiganensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella michiganensis.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella michiganensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..00c73868d07012a02c96757ad40a2a3c96d76311
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella michiganensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella oxytoca.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella oxytoca.npy
new file mode 100644
index 0000000000000000000000000000000000000000..d47816d99c4a153dc29c9056a5ba6f4146ac1a15
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella oxytoca.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella oxytoca.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella oxytoca.png
new file mode 100644
index 0000000000000000000000000000000000000000..e485f3d3ee872e6390f8fc83b2b8200968d38f86
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella oxytoca.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella pneumoniae.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella pneumoniae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e80c0c23903e7c17e6c1134f6b2568d2cb38f2c4
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella pneumoniae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella pneumoniae.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella pneumoniae.png
new file mode 100644
index 0000000000000000000000000000000000000000..5de8eb9f899995588837dfd6bbf99e3d2e41d030
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella pneumoniae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella quasipneumoniae.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella quasipneumoniae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..360af3e11e2b7efb81e22911d572319ba0ef5361
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella quasipneumoniae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella quasipneumoniae.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella quasipneumoniae.png
new file mode 100644
index 0000000000000000000000000000000000000000..5a692de8ab41bbce383247cc37647bd6f2f89de2
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella quasipneumoniae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella variicola.npy b/image_ref/img_ref_aligned_count_th_10/Klebsiella variicola.npy
new file mode 100644
index 0000000000000000000000000000000000000000..963f1662ed6e3664e40c39572cd17b89eafa40c7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella variicola.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Klebsiella variicola.png b/image_ref/img_ref_aligned_count_th_10/Klebsiella variicola.png
new file mode 100644
index 0000000000000000000000000000000000000000..f30e643550d6172fbba64f8ce67cbc3f69c60463
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Klebsiella variicola.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Morganella morganii.npy b/image_ref/img_ref_aligned_count_th_10/Morganella morganii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e5dcb829d2e1e7d0f4d27e548caa9d92ee859f98
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Morganella morganii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Morganella morganii.png b/image_ref/img_ref_aligned_count_th_10/Morganella morganii.png
new file mode 100644
index 0000000000000000000000000000000000000000..9fbbcbbd24f7143d50b89487d35df79d29f48948
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Morganella morganii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Pantoea agglomerans.npy b/image_ref/img_ref_aligned_count_th_10/Pantoea agglomerans.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2a4ac5f7b041a7d893bc8e96386921f66a2f9683
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Pantoea agglomerans.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Pantoea agglomerans.png b/image_ref/img_ref_aligned_count_th_10/Pantoea agglomerans.png
new file mode 100644
index 0000000000000000000000000000000000000000..02246a22ff8ca3a568390992f2a093069ce2291c
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Pantoea agglomerans.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Pantoea septica.npy b/image_ref/img_ref_aligned_count_th_10/Pantoea septica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..bf7f59e4cdef5164b8ce8899e0971ec5e3acbc2d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Pantoea septica.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Pantoea septica.png b/image_ref/img_ref_aligned_count_th_10/Pantoea septica.png
new file mode 100644
index 0000000000000000000000000000000000000000..c2e0ab42f86e186c3259d48f03044777d0a547e8
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Pantoea septica.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus columbae.npy b/image_ref/img_ref_aligned_count_th_10/Proteus columbae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..54074328d0bc0cdcbcf6e01e5672105c5f88b308
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus columbae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus columbae.png b/image_ref/img_ref_aligned_count_th_10/Proteus columbae.png
new file mode 100644
index 0000000000000000000000000000000000000000..ceabfb1cc6e6b6145d1720d44efc67690b720c0d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus columbae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus mirabilis.npy b/image_ref/img_ref_aligned_count_th_10/Proteus mirabilis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2e1a45206c7831c57f709cc026f927e0d04f2381
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus mirabilis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus mirabilis.png b/image_ref/img_ref_aligned_count_th_10/Proteus mirabilis.png
new file mode 100644
index 0000000000000000000000000000000000000000..18c2868b4c488ed8015a5b4f637b92bb37da2c75
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus mirabilis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus penneri.npy b/image_ref/img_ref_aligned_count_th_10/Proteus penneri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7803ce16d2ba0e9676b0365d8174e1126d707a2f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus penneri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus penneri.png b/image_ref/img_ref_aligned_count_th_10/Proteus penneri.png
new file mode 100644
index 0000000000000000000000000000000000000000..9e7d7d2928ee13f80e80ffa9d46e60dbf6e3b5b4
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus penneri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus terrae.npy b/image_ref/img_ref_aligned_count_th_10/Proteus terrae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..4d74864defd6dbaf3e2e1b9e65fbfc8b7b9f8ad7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus terrae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus terrae.png b/image_ref/img_ref_aligned_count_th_10/Proteus terrae.png
new file mode 100644
index 0000000000000000000000000000000000000000..ab8ff009e949179ed8227ed4a6db16e0720d8fb4
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus terrae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus vulgaris.npy b/image_ref/img_ref_aligned_count_th_10/Proteus vulgaris.npy
new file mode 100644
index 0000000000000000000000000000000000000000..1e4e5ebe2efb9c63bde6130504f64d9d989124bf
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus vulgaris.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Proteus vulgaris.png b/image_ref/img_ref_aligned_count_th_10/Proteus vulgaris.png
new file mode 100644
index 0000000000000000000000000000000000000000..a9836f0bfc4ed42e32e16edbe2f4d19aecf799e1
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Proteus vulgaris.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Providencia rettgeri.npy b/image_ref/img_ref_aligned_count_th_10/Providencia rettgeri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..81729dbb97961e27ff70e59197ecd1cf500932ac
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Providencia rettgeri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Providencia rettgeri.png b/image_ref/img_ref_aligned_count_th_10/Providencia rettgeri.png
new file mode 100644
index 0000000000000000000000000000000000000000..51266f6c4ffe914ef36fe419d2bddf419a6f529b
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Providencia rettgeri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Providencia stuartii.npy b/image_ref/img_ref_aligned_count_th_10/Providencia stuartii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..e7f29a077f7720d7ea0acb383f2db8df1bbb3fea
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Providencia stuartii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Providencia stuartii.png b/image_ref/img_ref_aligned_count_th_10/Providencia stuartii.png
new file mode 100644
index 0000000000000000000000000000000000000000..6d755e2473b9c79b56f9698e529ca793d397c08a
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Providencia stuartii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Raoultella ornithinolytica.npy b/image_ref/img_ref_aligned_count_th_10/Raoultella ornithinolytica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..16209a190525896b6ffa2ff3a1b771e30c083e5f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Raoultella ornithinolytica.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Raoultella ornithinolytica.png b/image_ref/img_ref_aligned_count_th_10/Raoultella ornithinolytica.png
new file mode 100644
index 0000000000000000000000000000000000000000..459772bb6fe803aac3d5b573d8ec1b535afe5e73
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Raoultella ornithinolytica.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Salmonella enterica.npy b/image_ref/img_ref_aligned_count_th_10/Salmonella enterica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..5c00bc3691e7dfe99b08f09463fcfe02a049b103
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Salmonella enterica.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Salmonella enterica.png b/image_ref/img_ref_aligned_count_th_10/Salmonella enterica.png
new file mode 100644
index 0000000000000000000000000000000000000000..512fc2dfdd098773593b353a8d8759839639f546
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Salmonella enterica.png differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Serratia marcescens.npy b/image_ref/img_ref_aligned_count_th_10/Serratia marcescens.npy
new file mode 100644
index 0000000000000000000000000000000000000000..4582d4c1ad54a7d452ab3ebba752b8473a11366c
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Serratia marcescens.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_10/Serratia marcescens.png b/image_ref/img_ref_aligned_count_th_10/Serratia marcescens.png
new file mode 100644
index 0000000000000000000000000000000000000000..cefa775013264c094359e2e8730ed491f297cbf0
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_10/Serratia marcescens.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter amalonaticus.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter amalonaticus.npy
new file mode 100644
index 0000000000000000000000000000000000000000..8d8fb75438d8c939d89294f9f458712a63e6c790
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter amalonaticus.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter amalonaticus.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter amalonaticus.png
new file mode 100644
index 0000000000000000000000000000000000000000..ff73a180afc9521bc83577da5dc74eccc82759ed
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter amalonaticus.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter braakii.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter braakii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..b99b551afefbf31c9df2096415bdfe91b48f29c8
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter braakii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter braakii.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter braakii.png
new file mode 100644
index 0000000000000000000000000000000000000000..3bf3fd75b84d7488f4012d2744c388e4214e56c0
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter braakii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter cronae.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter cronae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..c01f7c3180ad032bcc61a44f67c284b679db2eea
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter cronae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter cronae.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter cronae.png
new file mode 100644
index 0000000000000000000000000000000000000000..aee14767c6c990d6e3de9daada20748bf56f7b48
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter cronae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter farmeri.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter farmeri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..b74d3a578e4f48f8345633e1d37f239c66839030
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter farmeri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter farmeri.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter farmeri.png
new file mode 100644
index 0000000000000000000000000000000000000000..7def88eb5babbd2f116b58ad01c55bac7434ddc6
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter farmeri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter freundii.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter freundii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..bb23aa33cd20dfeb1618200530a7a2b45d0e0be3
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter freundii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter freundii.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter freundii.png
new file mode 100644
index 0000000000000000000000000000000000000000..591111d82e00e06e1874faab3c2603af8452ac0a
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter freundii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter koseri.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter koseri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..cb89ba0bcb17f5add37eed3bd52765eab7503613
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter koseri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter koseri.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter koseri.png
new file mode 100644
index 0000000000000000000000000000000000000000..e89e05c9210e415e4a9c3a7de47804b4675ea8f2
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter koseri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter portucalensis.npy b/image_ref/img_ref_aligned_count_th_5/Citrobacter portucalensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..750ba5095fdd34370c4f75fb5badcac650638fd8
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter portucalensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Citrobacter portucalensis.png b/image_ref/img_ref_aligned_count_th_5/Citrobacter portucalensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..84949e6a36ebb9ce2c353ec504eac0d7ce929027
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Citrobacter portucalensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter asburiae.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter asburiae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..54051204290132b65951a1a9efc4018eeb13f3a0
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter asburiae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter asburiae.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter asburiae.png
new file mode 100644
index 0000000000000000000000000000000000000000..4a6c689302e3cbfb1956c964f9097a8794758f74
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter asburiae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter bugandensis.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter bugandensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..557dc8a588d3f18098aaa48a6e400b9021771610
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter bugandensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter bugandensis.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter bugandensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..7bad33e7b4624fa42ab0a9377b0c2a577110d48d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter bugandensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter chengduensis.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter chengduensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..9c2838e258696d55924ef6675eafeb9eee5b4907
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter chengduensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter chengduensis.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter chengduensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..32e1695c14270ef2400793e7f75286e9d4dc6c0f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter chengduensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter cloacae.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter cloacae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..4aab43d99ee27ef08b14eb9017a0156ebb4f121f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter cloacae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter cloacae.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter cloacae.png
new file mode 100644
index 0000000000000000000000000000000000000000..3427efe8b078fb195a8d2a96862a3db1fb9baf96
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter cloacae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter hormaechei.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter hormaechei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..8345b9962c1f8ce7e3f92065010ebf0c958c5f24
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter hormaechei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter hormaechei.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter hormaechei.png
new file mode 100644
index 0000000000000000000000000000000000000000..7b65c935d2301f31e6f8b5fa52141aa1cea2278d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter hormaechei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter kobei.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter kobei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..711cca3e904a5ba6683d5f9620d11fa63fe1731a
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter kobei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter kobei.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter kobei.png
new file mode 100644
index 0000000000000000000000000000000000000000..a56c769ff99e539244f759c57ad29e00edb18fe1
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter kobei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter ludwigii.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter ludwigii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..a9fe7a5bde7c8661aadbefa1761706dd748c8f14
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter ludwigii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter ludwigii.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter ludwigii.png
new file mode 100644
index 0000000000000000000000000000000000000000..f0e5b07d3c25722ee983846940327e2fa6b3a205
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter ludwigii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter roggenkampii.npy b/image_ref/img_ref_aligned_count_th_5/Enterobacter roggenkampii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..5fc965f07819868b4f6f64d0f35b0c974b2d25c4
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter roggenkampii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Enterobacter roggenkampii.png b/image_ref/img_ref_aligned_count_th_5/Enterobacter roggenkampii.png
new file mode 100644
index 0000000000000000000000000000000000000000..64c8378f96f7a27fb71247f3942b9a2e83fe3fc7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Enterobacter roggenkampii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Escherichia coli.npy b/image_ref/img_ref_aligned_count_th_5/Escherichia coli.npy
new file mode 100644
index 0000000000000000000000000000000000000000..896899a96bb853575d0e92f221f919b8f568428c
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Escherichia coli.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Escherichia coli.png b/image_ref/img_ref_aligned_count_th_5/Escherichia coli.png
new file mode 100644
index 0000000000000000000000000000000000000000..200ad073c45e7817b9e49b0f4e4a93000685a0c5
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Escherichia coli.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Hafnia alvei.npy b/image_ref/img_ref_aligned_count_th_5/Hafnia alvei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..2494726d4b50e324d0dd1dfbf5e828472da490f8
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Hafnia alvei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Hafnia alvei.png b/image_ref/img_ref_aligned_count_th_5/Hafnia alvei.png
new file mode 100644
index 0000000000000000000000000000000000000000..bc2aa902043c9b38a260023c6b9f2dc883384969
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Hafnia alvei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Hafnia paralvei.npy b/image_ref/img_ref_aligned_count_th_5/Hafnia paralvei.npy
new file mode 100644
index 0000000000000000000000000000000000000000..460b1cdbf265a06bf0e96457ba03b7589d40714f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Hafnia paralvei.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Hafnia paralvei.png b/image_ref/img_ref_aligned_count_th_5/Hafnia paralvei.png
new file mode 100644
index 0000000000000000000000000000000000000000..579d5b5df6a6ddd0c6f266f4f2ce0e369eb962b2
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Hafnia paralvei.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella aerogenes.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella aerogenes.npy
new file mode 100644
index 0000000000000000000000000000000000000000..03ffa5e2b61351a0c02714d78470e37b923daf5f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella aerogenes.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella aerogenes.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella aerogenes.png
new file mode 100644
index 0000000000000000000000000000000000000000..942cf0e2b8b19eedddfb9ebd4ab116635b4a5e86
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella aerogenes.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella grimontii.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella grimontii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..44dcdd2868e6160df9d54893b78c1bd7bfd5200c
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella grimontii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella grimontii.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella grimontii.png
new file mode 100644
index 0000000000000000000000000000000000000000..b5c052086580f33595bc5443951ffd8bcf5baaab
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella grimontii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella michiganensis.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella michiganensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..02d90fcd9f0336863b69264ebb2132dd78caa053
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella michiganensis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella michiganensis.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella michiganensis.png
new file mode 100644
index 0000000000000000000000000000000000000000..f42a9190f2099b48a0f9090e2269e29b41b6eb28
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella michiganensis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella oxytoca.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella oxytoca.npy
new file mode 100644
index 0000000000000000000000000000000000000000..a541af94c644b5c3fdf7e5d4d95a537359cbb588
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella oxytoca.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella oxytoca.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella oxytoca.png
new file mode 100644
index 0000000000000000000000000000000000000000..d290af4870a57e666fcc49919ab117945709b2fe
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella oxytoca.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella pneumoniae.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella pneumoniae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..dbdfa45ead45c6cef188f7e310b2683892ea7c5f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella pneumoniae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella pneumoniae.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella pneumoniae.png
new file mode 100644
index 0000000000000000000000000000000000000000..47c099be49a76d900f531ea37a93ac8bfe13a9c3
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella pneumoniae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella quasipneumoniae.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella quasipneumoniae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..46d6b0ce1a2543939271115993b6461fe17b4f7d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella quasipneumoniae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella quasipneumoniae.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella quasipneumoniae.png
new file mode 100644
index 0000000000000000000000000000000000000000..658a33a38d5d25be38f5771bc5f628b23e571fba
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella quasipneumoniae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella variicola.npy b/image_ref/img_ref_aligned_count_th_5/Klebsiella variicola.npy
new file mode 100644
index 0000000000000000000000000000000000000000..8a92e7e252de0dd2009a3f130201b07b63f8253d
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella variicola.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Klebsiella variicola.png b/image_ref/img_ref_aligned_count_th_5/Klebsiella variicola.png
new file mode 100644
index 0000000000000000000000000000000000000000..4c453e885cfe951a78ed45a59adc244b5e8d2b51
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Klebsiella variicola.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Morganella morganii.npy b/image_ref/img_ref_aligned_count_th_5/Morganella morganii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..28cf265ad96479f3bb7918efdd26ddddb83294a7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Morganella morganii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Morganella morganii.png b/image_ref/img_ref_aligned_count_th_5/Morganella morganii.png
new file mode 100644
index 0000000000000000000000000000000000000000..5407a4c4cd1241067ea1853ddbf97b3fca256a5b
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Morganella morganii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Pantoea agglomerans.npy b/image_ref/img_ref_aligned_count_th_5/Pantoea agglomerans.npy
new file mode 100644
index 0000000000000000000000000000000000000000..173e03642abdbd26144c76d3291e89edc1e2b6fd
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Pantoea agglomerans.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Pantoea agglomerans.png b/image_ref/img_ref_aligned_count_th_5/Pantoea agglomerans.png
new file mode 100644
index 0000000000000000000000000000000000000000..8f5dfaf32d4ac5d1a1a4bf1dec9e7a424812ec3b
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Pantoea agglomerans.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Pantoea septica.npy b/image_ref/img_ref_aligned_count_th_5/Pantoea septica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..d370ccce931da740080496431ebae478c6530b27
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Pantoea septica.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Pantoea septica.png b/image_ref/img_ref_aligned_count_th_5/Pantoea septica.png
new file mode 100644
index 0000000000000000000000000000000000000000..05e40aa009cfcf1fd14ca6c107402628b9723c62
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Pantoea septica.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus columbae.npy b/image_ref/img_ref_aligned_count_th_5/Proteus columbae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..ff4e3559a4038ea79a4a1fdece4a9f0bf9dbaa12
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus columbae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus columbae.png b/image_ref/img_ref_aligned_count_th_5/Proteus columbae.png
new file mode 100644
index 0000000000000000000000000000000000000000..eff84bf6436681f10f5d46437fbdacf6de77b375
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus columbae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus mirabilis.npy b/image_ref/img_ref_aligned_count_th_5/Proteus mirabilis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..c8fd2c365a3e5bd2340dd75d0b8c4d8d672d7544
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus mirabilis.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus mirabilis.png b/image_ref/img_ref_aligned_count_th_5/Proteus mirabilis.png
new file mode 100644
index 0000000000000000000000000000000000000000..9680554b5cf285b57cf86fa0bfdccfffa7365b01
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus mirabilis.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus penneri.npy b/image_ref/img_ref_aligned_count_th_5/Proteus penneri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..c3ed3231632a3ec3da00f8f6d2ef9c5e48fb766b
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus penneri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus penneri.png b/image_ref/img_ref_aligned_count_th_5/Proteus penneri.png
new file mode 100644
index 0000000000000000000000000000000000000000..8932b6fbcd8a10e35d53cc160c202549c06265ae
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus penneri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus terrae.npy b/image_ref/img_ref_aligned_count_th_5/Proteus terrae.npy
new file mode 100644
index 0000000000000000000000000000000000000000..cbbab0076d3e6435404bd70a9a70126ec04b5e00
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus terrae.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus terrae.png b/image_ref/img_ref_aligned_count_th_5/Proteus terrae.png
new file mode 100644
index 0000000000000000000000000000000000000000..1d800138578570573336af07af22733ec64271ef
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus terrae.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus vulgaris.npy b/image_ref/img_ref_aligned_count_th_5/Proteus vulgaris.npy
new file mode 100644
index 0000000000000000000000000000000000000000..18698177a7a5c66d211cca2a67b8ddb9bf9ce83f
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus vulgaris.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Proteus vulgaris.png b/image_ref/img_ref_aligned_count_th_5/Proteus vulgaris.png
new file mode 100644
index 0000000000000000000000000000000000000000..297fa506214e56f9921cf0a269544e9f07f46454
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Proteus vulgaris.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Providencia rettgeri.npy b/image_ref/img_ref_aligned_count_th_5/Providencia rettgeri.npy
new file mode 100644
index 0000000000000000000000000000000000000000..d53e9dbb20d7dbe3e5557161cd31bddacbf32bf3
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Providencia rettgeri.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Providencia rettgeri.png b/image_ref/img_ref_aligned_count_th_5/Providencia rettgeri.png
new file mode 100644
index 0000000000000000000000000000000000000000..84674694bebfcb6539248bd16fd207c0bfaa9126
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Providencia rettgeri.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Providencia stuartii.npy b/image_ref/img_ref_aligned_count_th_5/Providencia stuartii.npy
new file mode 100644
index 0000000000000000000000000000000000000000..ae9fcaeb0ba2548e3177677ba337e647758710d7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Providencia stuartii.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Providencia stuartii.png b/image_ref/img_ref_aligned_count_th_5/Providencia stuartii.png
new file mode 100644
index 0000000000000000000000000000000000000000..3a500d0f4464679837974cbe7048b1d033cad7a7
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Providencia stuartii.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Raoultella ornithinolytica.npy b/image_ref/img_ref_aligned_count_th_5/Raoultella ornithinolytica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7c0554e8449cf512b7a7aa3a1c25abc83c432eaa
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Raoultella ornithinolytica.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Raoultella ornithinolytica.png b/image_ref/img_ref_aligned_count_th_5/Raoultella ornithinolytica.png
new file mode 100644
index 0000000000000000000000000000000000000000..86acbdf4a53e56557cdf6fb3caebabfeb0d2f95b
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Raoultella ornithinolytica.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Salmonella enterica.npy b/image_ref/img_ref_aligned_count_th_5/Salmonella enterica.npy
new file mode 100644
index 0000000000000000000000000000000000000000..535ea8ddb30dde4bb4c72dc86388854edacd7a8b
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Salmonella enterica.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Salmonella enterica.png b/image_ref/img_ref_aligned_count_th_5/Salmonella enterica.png
new file mode 100644
index 0000000000000000000000000000000000000000..1d00e58264b8b68bfecaca67f1f4fe06c335586c
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Salmonella enterica.png differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Serratia marcescens.npy b/image_ref/img_ref_aligned_count_th_5/Serratia marcescens.npy
new file mode 100644
index 0000000000000000000000000000000000000000..9582e5f8ae86e732f8c2834d81fa18288f690973
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Serratia marcescens.npy differ
diff --git a/image_ref/img_ref_aligned_count_th_5/Serratia marcescens.png b/image_ref/img_ref_aligned_count_th_5/Serratia marcescens.png
new file mode 100644
index 0000000000000000000000000000000000000000..9f9252d404df17de6d11aa69af566c4ccb86e4f1
Binary files /dev/null and b/image_ref/img_ref_aligned_count_th_5/Serratia marcescens.png differ
diff --git a/image_ref/utils.py b/image_ref/utils.py
index 097d8961fce1da755a59019f8cf0e024e996eeac..f457be5efb99373c6106d841f0a7207658472ab3 100644
--- a/image_ref/utils.py
+++ b/image_ref/utils.py
@@ -8,6 +8,7 @@ from matplotlib_venn import venn2
 from analyse_diann_digestion import load_lib
 import matplotlib.image as mpimg
 import re
+from loess.loess_1d import loess_1d
 
 # SPECIES = [f.name for f in os.scandir('../data/processed_data_wiff/npy_image/all data') if f.is_dir()]
 SPECIES = ['Enterobacter bugandensis', 'Enterobacter hormaechei', 'Enterobacter cloacae',
@@ -138,8 +139,7 @@ def build_ref_image_from_diann(path_parqet, ms1_end_mz, ms1_start_mz, bin_mz, ma
     return im
 
 
-def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_start_mz, bin_mz, max_cycle, min_rt=None,
-                                      max_rt=None):
+def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_start_mz, bin_mz, max_cycle, path_ref_alignment):
     df = load_lib(path_parqet)
     df = df[['Stripped.Sequence', 'Precursor.Charge', 'RT', 'Precursor.Mz']]
     df = df[df['Stripped.Sequence'].isin(target_seq)]
@@ -148,24 +148,26 @@ def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_s
     total_ms1_mz = ms1_end_mz - ms1_start_mz
     n_bin_ms1 = int(total_ms1_mz // bin_mz)
     im = np.zeros([max_cycle, n_bin_ms1])
-    if max_rt is None:
-        max_rt = np.max(df_unique['RT'])
-    if min_rt is None:
-        min_rt = np.min(df_unique['RT'])
-    total_rt = max_rt - min_rt + 1e-3
+
+    lib = pd.read_csv(path_ref_alignment, sep='\t')
+    xout, yout, wout = loess_1d(np.array(lib['Predicted.iRT'].tolist()), np.array(lib['Predicted.RT'].tolist()),
+                                xnew=df_unique['RT'],
+                                degree=1,
+                                npoints=None, rotate=False, sigy=None)
+    df_unique['Aligned_RT']=yout
     for row in df_unique.iterrows():
-        if 900 > int(((row[1]['Precursor.Mz'] - ms1_start_mz) / total_ms1_mz) * n_bin_ms1) >= 0:
-            im[int((row[1]['RT'] - min_rt) / total_rt * max_cycle), int(
+        if 900 > int(((row[1]['Precursor.Mz'] - ms1_start_mz) / total_ms1_mz) * n_bin_ms1) >= 0 and int((row[1]['Aligned_RT']/11.51) * max_cycle) <663:
+            im[int((row[1]['Aligned_RT']/11.51) * max_cycle), int(
                 ((row[1]['Precursor.Mz'] - ms1_start_mz) / total_ms1_mz) * n_bin_ms1)] = 1
 
     return im
 
 
 if __name__ == '__main__':
-    df = load_lib('fasta/global_peptide_list.parquet')
+    # df = load_lib('fasta/global_peptide_list.parquet')
     # df = build_database_ref_peptide()
     # df.to_csv("dataset_species_ref_peptides.csv", index=False)
-    # Write fasta file
+    # Write fasta fi#le
     # with open('fasta/optimal peptide set/gobal_peptide_set.fasta', "w") as f:
     #     df_spe = df[df['Specie'].isin(SPECIES)]
     #     spe_list = df_spe['Sequence'].drop_duplicates().to_list()
@@ -173,8 +175,8 @@ if __name__ == '__main__':
     #     for pep in spe_list :
     #         print(pep)
     #         f.write(pep+'\n')
-    #
-    # df_count = compute_common_peptide("dataset_species_ref_peptides.csv", SPECIES)
+
+    df_count = compute_common_peptide("dataset_species_ref_peptides.csv", SPECIES)
     #
     # #
     # # Create ref img
@@ -183,15 +185,15 @@ if __name__ == '__main__':
     # min_rt = df_full['RT'].min()
     # max_rt = df_full['RT'].max()
     # #
-    # df = pd.read_csv("dataset_species_ref_peptides.csv")
-    # #
-    # for spe in SPECIES:
-    #     print(spe)
-    #     df_spe = df[df['Specie'] == spe]
-    #     df_spec_no_common = df_spe[df_spe['Sequence'].isin(df_count[df_count['Count']<5]['Sequence'])]
-    #     im = build_ref_image_from_diann_global(
-    #         'fasta/global_peptide_list.parquet', target_seq=df_spec_no_common['Sequence'].to_list(), ms1_end_mz=1250,
-    #         ms1_start_mz=350, bin_mz=1, max_cycle=663, min_rt=min_rt, max_rt=max_rt)
-    #     plt.clf()
-    #     mpimg.imsave('img_ref_count_th_5/' + spe + '.png', im)
-    #     np.save('img_ref_count_th_5/' + spe + '.npy', im)
+    df = pd.read_csv("dataset_species_ref_peptides.csv")
+    #
+    for spe in SPECIES:
+        print(spe)
+        df_spe = df[df['Specie'] == spe]
+        # df_spec_no_common = df_spe[df_spe['Sequence'].isin(df_count[df_count['Count']<10]['Sequence'])]
+        im = build_ref_image_from_diann_global(
+            'fasta/global_peptide_list.parquet', target_seq=df_spe['Sequence'].to_list(), ms1_end_mz=1250,
+            ms1_start_mz=350, bin_mz=1, max_cycle=663, path_ref_alignment='report_coli_95_97_98.tsv')
+        plt.clf()
+        mpimg.imsave('img_ref_aligned/' + spe + '.png', im)
+        np.save('img_ref_aligned/' + spe + '.npy', im)