diff --git a/image_processing/build_image.py b/image_processing/build_image.py
index 7c4934c70d489e0bd92b87d7e5d63928f20ea594..97e11ed6f5dcbc50a5f0f392193bde1f399eabfe 100644
--- a/image_processing/build_image.py
+++ b/image_processing/build_image.py
@@ -15,7 +15,7 @@ def build_image_ms1_wiff(path, bin_mz):
             ms1_end_mz = rawFile.source.ScanInfos[scanNumber].HighMz
             max_cycle+=1
 
-    # print('start', ms1_start_mz, 'end', ms1_end_mz)
+    print('start', ms1_start_mz, 'end', ms1_end_mz)
     total_ms1_mz = ms1_end_mz - ms1_start_mz
 
     n_bin_ms1 = int(total_ms1_mz // bin_mz)
diff --git a/image_ref/img_ref/Citrobacter amalonaticus.npy b/image_ref/img_ref/Citrobacter amalonaticus.npy
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diff --git a/image_ref/img_ref/Citrobacter braakii.npy b/image_ref/img_ref/Citrobacter braakii.npy
index 4515158d627950404e789042f7a40e9f6f6e6d72..d2b92ca77ed84baa84f17f41331b1098c361aae6 100644
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index 2aced6df0f2011095a138ce58b829555203081e5..797005855759247292082d9f1b7911d3cc52f0db 100644
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diff --git a/image_ref/img_ref/Citrobacter cronae.npy b/image_ref/img_ref/Citrobacter cronae.npy
index cf4901a132b47a1f733905237501cf71c2433ab1..6445621ea39bf9380a11cf3d8aebe3a2422f005f 100644
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index ccbaac9b8e756fb9dfafd4f704533b7f07ea19c9..caea8ae4295d9102d19431af041f68a443c35fbb 100644
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diff --git a/image_ref/img_ref/Citrobacter farmeri.npy b/image_ref/img_ref/Citrobacter farmeri.npy
index f197b91d39e57aed183d5cc1ffb1193765f9caad..4bf29b99a2aa7301536d1138fa6cd1744a277e34 100644
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index 97a6c6e23aaa5a970bf6691d879866ab626dcb8f..6302dd34825b44a8d50768ab8a35f879dbcf61ba 100644
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diff --git a/image_ref/img_ref/Citrobacter freundii.npy b/image_ref/img_ref/Citrobacter freundii.npy
index 9edcae93f12cb1afcc253a6ee7ea0ca106d9c368..6cbe637e1482b09aa0d3eb0ea102d471d4ed2949 100644
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diff --git a/image_ref/img_ref/Citrobacter freundii.png b/image_ref/img_ref/Citrobacter freundii.png
index bb0c83b2c79f37c029b02ac7ea3ff3515e8f7729..160fc71e2aafa30db2226ac13def5f209bc586cc 100644
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diff --git a/image_ref/img_ref/Citrobacter koseri.npy b/image_ref/img_ref/Citrobacter koseri.npy
index 16d363b4e65cf5039bd113ac6cd44fb226ea2f42..39fb637f146691710cd68f2ccfb081a3969fae08 100644
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diff --git a/image_ref/img_ref/Citrobacter portucalensis.npy b/image_ref/img_ref/Citrobacter portucalensis.npy
index 0fbf5dc8795b0a2d958f1bfb09c3c613a0868877..0c59ab2200aa2bd9e6903446c5d32f03b5439f86 100644
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index 578a68ae15d64a0bf6da3a860aad0e7e1cd33d94..352dfd49d10131f6251a05b4c18e63e655b1bbca 100644
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diff --git a/image_ref/img_ref/Enterobacter asburiae.npy b/image_ref/img_ref/Enterobacter asburiae.npy
index 30cad59165bd03aaff4794aee74d69b4c2b8d9a5..fa05f34e8929f52f20b41d5c73bdedff61fd609f 100644
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index 490c02c0644b5d485056e2f11accc6a58ba7b824..0757ab13efb8a92ec651b8914cbc204bee954248 100644
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diff --git a/image_ref/img_ref/Enterobacter bugandensis.npy b/image_ref/img_ref/Enterobacter bugandensis.npy
new file mode 100644
index 0000000000000000000000000000000000000000..7b5bd4fa0fdd3f46a82b08d8595ff0b402a866c3
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diff --git a/image_ref/img_ref/Enterobacter bugandensis.png b/image_ref/img_ref/Enterobacter bugandensis.png
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index 0000000000000000000000000000000000000000..9229e60106563f758a6f482f26fb3ca29b256df0
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index d0e2d96401097e3a53cfc947327f941f59d99b5e..2c9f7782b1bf40f1a2d55891ce059f29de66c5e2 100644
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index 8f9026dfb8f926fd97c53be594f9a47682ba47d0..2ef782de7b56e242ee0fdd662a727a0adc5a605b 100644
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diff --git a/image_ref/img_ref/Enterobacter cloacae.npy b/image_ref/img_ref/Enterobacter cloacae.npy
index 049ca997e4c622c670e738ae793437657a6ed05e..59d43c57f10104809cd993bcda1165dc3574e4d1 100644
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index c41068e600376b60b649d11dd33a285c25aeb0fb..92942b870525aeef7b04b57f453d95d69a6dd562 100644
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index 633057f00780be8852cda8d4b52782b5c51377b0..c3f49850ba465ccbf7a5ef38aee48cd77d9269d3 100644
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index 13392cace8b16b8022ac0edeee78b88ab5650743..05242c12de3b78caa8d35f3f9116ecf22aec4e6e 100644
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index 31a4cbd9adb00f469c57f91285f746ccbac2beab..f473ea367490c121d01cd9320d8a4f2d480c2ef8 100644
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diff --git a/image_ref/img_ref/Enterobacter ludwigii.npy b/image_ref/img_ref/Enterobacter ludwigii.npy
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index 0000000000000000000000000000000000000000..5730af70ce7bcb4a46c04e8297cb5bcfe6aebdf6
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diff --git a/image_ref/img_ref/Enterobacter roggenkampii.npy b/image_ref/img_ref/Enterobacter roggenkampii.npy
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index 0000000000000000000000000000000000000000..9de63525d9062e67027ab8434b0b7e78dbcba432
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index 0000000000000000000000000000000000000000..848ec0ec6cc926ca9de6bba04e508753ef5955e0
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diff --git a/image_ref/img_ref/Escherichia coli.npy b/image_ref/img_ref/Escherichia coli.npy
index d2941309a944196a491bb35c5dfed005be5c05f3..e6854173418927adb515e695608f901c8bd20b7b 100644
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index c3500a11d55f642854be8bf6e65ebd886cd1d9ac..29ead59828f85626a0545071b85c521b50dc9ed8 100644
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index 701ad33c6557d615d252a6dfcf5f233743e9780c..d87b322e9a7da9c9422a950b9454bb997406a315 100644
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diff --git a/image_ref/utils.py b/image_ref/utils.py
index bebd1b433e7de6401080cb93e415d95bd89b7fbf..f9a326908d872723d607f8b3ce97cf4fd4f58f7a 100644
--- a/image_ref/utils.py
+++ b/image_ref/utils.py
@@ -1,3 +1,5 @@
+import os
+
 import fastapy
 import matplotlib.pyplot as plt
 import numpy as np
@@ -7,13 +9,21 @@ from analyse_diann_digestion import load_lib
 import matplotlib.image as mpimg
 import re
 
-SPECIES = ['Citrobacter cronae', 'Citrobacter portucalensis', 'Enterobacter hormaechei', 'Klebsiella aerogenes',
-                'Klebsiella variicola', 'Raoultella ornithinolytica', 'Citrobacter farmeri', 'Enterobacter asburiae',
-                'Enterobacter kobei', 'Klebsiella michiganensis', 'Morganella morganii', 'Salmonella enterica',
-                'Citrobacter amalonaticus', 'Citrobacter freundii', 'Enterobacter chengduensis', 'Escherichia coli',
-                'Klebsiella oxytoca', 'Proteus mirabilis', 'Serratia marcescens', 'Citrobacter braakii',
-                'Citrobacter koseri', 'Enterobacter cloacae', 'Hafnia alvei', 'Klebsiella pneumoniae',
-                'Providencia stuartii']
+# 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',
+           'Serratia marcescens', 'Morganella morganii', 'Citrobacter freundii', 'Hafnia alvei',
+           'Citrobacter amalonaticus', 'Salmonella enterica', 'Klebsiella quasipneumoniae',
+           'Raoultella ornithinolytica', 'Escherichia coli', 'Hafnia paralvei', 'Citrobacter portucalensis',
+           'Proteus penneri', 'Providencia stuartii',
+           'Klebsiella michiganensis', 'Klebsiella variicola', 'Proteus terrae', 'Pantoea septica',
+           'Proteus vulgaris', 'Proteus mirabilis', 'Klebsiella oxytoca',
+           'Klebsiella aerogenes', 'Proteus columbae',
+           'Citrobacter koseri', 'Enterobacter kobei',
+           'Klebsiella pneumoniae', 'Pantoea agglomerans', 'Klebsiella grimontii',
+           'Providencia rettgeri',
+           'Citrobacter farmeri', 'Enterobacter chengduensis', 'Enterobacter ludwigii',
+           'Enterobacter asburiae', 'Citrobacter braakii', 'Enterobacter roggenkampii', 'Citrobacter cronae']
+
 
 # trypsin cut after K or R (if not followed by P)
 
@@ -72,7 +82,7 @@ def build_database_ref_peptide():
         for line in f:
             if line != '\n':
                 if '>' in line:
-                    #remove new line
+                    # remove new line
                     line = line.replace('\n', '')
 
                     # typo ??
@@ -90,19 +100,20 @@ def build_database_ref_peptide():
                     o = split_line[3].replace('_', ' ')
                 else:
                     seq = line.split(' ')[1]
-                    #remove new lines
-                    seq = seq.replace('\n','')
+                    # remove new lines
+                    seq = seq.replace('\n', '')
                     l.append({'Sequence': seq, 'Protein code': prot, 'Error treshold': err, 'Prevalance': prev,
                               'Specie': spe, 'Genus': gen, 'Family': fam, 'Order': o})
     df = pd.DataFrame(l)
     return df.drop_duplicates()
 
-def compute_common_peptide(df_path,species):
+
+def compute_common_peptide(df_path, species):
     df = pd.read_csv(df_path)
     df_filter = df[df['Specie'].isin(species)]
-    df_filter = df_filter[['Sequence','Specie']].drop_duplicates()
+    df_filter = df_filter[['Sequence', 'Specie']].drop_duplicates()
     df_filter['Count'] = df_filter.groupby('Sequence')['Sequence'].transform('count')
-    df_count = df_filter[['Sequence','Count']].drop_duplicates()
+    df_count = df_filter[['Sequence', 'Count']].drop_duplicates()
     return df_count
 
 
@@ -126,7 +137,9 @@ 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, min_rt=None,
+                                      max_rt=None):
     df = load_lib(path_parqet)
     df = df[['Stripped.Sequence', 'Precursor.Charge', 'RT', 'Precursor.Mz']]
     df = df[df['Stripped.Sequence'].isin(target_seq)]
@@ -151,29 +164,32 @@ def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_s
 if __name__ == '__main__':
     # df = build_database_ref_peptide()
     # df.to_csv("dataset_species_ref_peptides.csv", index=False)
-    # #Write fasta file
+    # Write fasta file
     # with open('fasta/optimal peptide set/gobal_peptide_set.fasta', "w") as f:
-    #     for spe in SPECIES:
-    #         df_spe = df[df['Specie']==spe]
-    #         spe_list = df_spe['Sequence'].drop_duplicate().to_list()
-    #         if not spe_list:
-    #             print('Empty : ',spe)
-    #         for pep in spe_list :
-    #             f.write(pep)
-
-    df_count = compute_common_peptide("dataset_species_ref_peptides.csv", SPECIES)
-
+    #     df_spe = df[df['Specie'].isin(SPECIES)]
+    #     spe_list = df_spe['Sequence'].drop_duplicates().to_list()
     #
-    #Create ref img
-    # df_full = load_lib(
-    #     'fasta/full proteom/steigerwaltii variants/uniparc_proteome_UP000033376_2025_03_14.predicted.parquet')
-    # min_rt = df_full['RT'].min()
-    # max_rt = df_full['RT'].max()
+    #     for pep in spe_list :
+    #         print(pep)
+    #         f.write(pep+'\n')
+    #
+    # df_count = compute_common_peptide("dataset_species_ref_peptides.csv", SPECIES)
+
     #
-    # for spe in SPECIES:
-    #     im = build_ref_image_from_diann(
-    #         'fasta/optimal peptide set/' + spe + '.parquet', 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/' + spe + '.png', im)
-    #     np.save(spe + '.npy', im)
+    # Create ref img
+    df_full = load_lib(
+        'fasta/full proteom/steigerwaltii variants/uniparc_proteome_UP000033376_2025_03_14.predicted.parquet')
+    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]
+        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, min_rt=min_rt, max_rt=max_rt)
+        plt.clf()
+        mpimg.imsave('img_ref/' + spe + '.png', im)
+        np.save('img_ref/' + spe + '.npy', im)