Adding multiple reagent configurations and supporting material.

IBEXImagingCommunity · Feb 9, 2024 · 9819c9d · 9819c9d
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diff --git a/.zenodo.json b/.zenodo.json
@@ -112,6 +112,11 @@
             "name": "Koenig, Joshua F. E.",
             "orcid": "0000-0002-8909-5039"
         },
+        {
+            "affiliation": "National Institutes of Health",
+            "name": "Makranz, Chen",
+            "orcid": "0000-0002-6944-6997"
+        },
         {
             "affiliation": "McMaster University",
             "name": "Murakami Olyntho, Vitoria",

diff --git a/data/reagent_resources.csv b/data/reagent_resources.csv
@@ -1062,3 +1062,14 @@ P49840,Primary Antibody,Phospho-GSK-3alpha,Human,Rabbit,IgG,36E9,Cell Signaling
 Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
 P08575,Primary Antibody,CD45,Human,Mouse,IgG1,2B11 + PD7/26,Novus Biologicals,NBP2-34528AF700,AF700,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
 Q6FHL8,Primary Antibody,CTGF,Human,Rabbit,IgG,OT11F4,FabGennix,CTGF-FITC,FITC,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
+E9PVX6,Primary Antibody,Ki-67,Mouse,Rat,IgG2a,SolA15,Thermo Fisher Scientific,606-5698-82,AF660,AB_2896286,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+Q08481,Primary Antibody,CD31,Mouse,Rat,IgG2a,MEC13.3,BioLegend,102515,AF647,AB_2161030,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+P06332,Primary Antibody,CD4,Mouse,Rat,IgG2a,RM4-5,BioLegend,100533,AF647,AB_493372,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+P06332,Primary Antibody,CD4,Mouse,Rat,IgG2a,RM4-5,BioLegend,100533,AF647,AB_493372,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Spleen,Healthy,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+NA,Primary Antibody,mCherrry,Mouse,Chicken,IgY,polyclonal,Novus Biologicals,NBP2-25158,NA,AB_2636881,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+Q9EQX4,Primary Antibody,Iba-1,Mouse,Rabbit,IgG,polyclonal,FUJIFILM Wako Chemicals U.S.A. Corporation,019-19741,NA,AB_839504,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+P63158,Primary Antibody,CXCL12,Mouse,Rabbit,IgG,polyclonal,Abcam,AB25117,NA,AB_2088164,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+P70658,Primary Antibody,CXCR4,Mouse,Rabbit,IgG,polyclonal,Novus Biologicals,NB-100 74396,NA,AB_1048484,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+P56485,Primary Antibody,CXCR7,Mouse,Rabbit,IgG,polyclonal,Novus Biologicals,NBP2-24779G,DyLight 488,NA,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+Q9QXH4,Primary Antibody,CD11c,Mouse,Armenian Hamster,IgG,N418,BioLegend,117314,AF647,AB_492850,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
+P03995,Primary Antibody,GFAP,Mouse,Mouse,IgG1,GA5,Thermo Fisher Scientific,41-9892-82,eF570,AB_2573656,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3%  Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
diff --git a/data/vendor_urls.csv b/data/vendor_urls.csv
@@ -26,4 +26,6 @@ IBT BioServices,https://www.ibtbioservices.com/
 Cell IDx,https://cellidx.com/
 Vector Laboratories,https://vectorlabs.com/
 Agilent,https://www.agilent.com/en/dako-products
-FabGennix,https://fabgennix.com/
+FabGennix,https://fabgennix.com/
+Synaptic Systems,https://www.sysy.com/
+FUJIFILM Wako Chemicals U.S.A. Corporation,https://labchem-wako.fujifilm.com
diff --git a/docs/supporting_material/CD11c_AF647/0000-0002-6944-6997.md b/docs/supporting_material/CD11c_AF647/0000-0002-6944-6997.md
@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism    | Isotype   | Clonality   | Vendor    |   Catalog Number | Conjugate   | RRID      | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:-----------------|:----------|:------------|:----------|-----------------:|:------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| Q9QXH4                     | Primary Antibody | CD11c                             | Mouse            | Armenian Hamster | IgG       | N418        | BioLegend |           117314 | AF647       | AB_492850 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:25.
+
+| Mouse Spleen Hochest (Blue) CD11c (Magenta Biolegend #117314) |
+|:-------:|
+| ![](Mouse_Spleen_Hochest_Blue_CD11c_Magenta_Biolegend_117314.jpg) |
diff --git a/...terial/CD11c_AF647/Mouse_Spleen_Hochest_Blue_CD11c_Magenta_Biolegend_117314.jpg b/...terial/CD11c_AF647/Mouse_Spleen_Hochest_Blue_CD11c_Magenta_Biolegend_117314.jpg
diff --git a/docs/supporting_material/CD31_AF647/0000-0002-6944-6997.md b/docs/supporting_material/CD31_AF647/0000-0002-6944-6997.md
@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   | Clonality   | Vendor    |   Catalog Number | Conjugate   | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| Q08481                     | Primary Antibody | CD31                              | Mouse            | Rat             | IgG2a     | MEC13.3     | BioLegend |           102515 | AF647       | AB_2161030 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:100.
+
+| Mouse Brain Tumor Hochest(Blue) mCherry (Green Novus #NBP2-25158) CD31(Magenta Biolegend #102515) |
+|:-------:|
+| ![](Mouse_Brain_Tumor_Hochest_Blue_mCherry_Green_Novus_NBP2_25158_CD31_Magenta_Biolegend_102515.jpg) |
diff --git a/...r_Hochest_Blue_mCherry_Green_Novus_NBP2_25158_CD31_Magenta_Biolegend_102515.jpg b/...r_Hochest_Blue_mCherry_Green_Novus_NBP2_25158_CD31_Magenta_Biolegend_102515.jpg
diff --git a/docs/supporting_material/CD4_AF647/0000-0002-6944-6997.md b/docs/supporting_material/CD4_AF647/0000-0002-6944-6997.md
@@ -0,0 +1,28 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   | Clonality   | Vendor    |   Catalog Number | Conjugate   | RRID      | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P06332                     | Primary Antibody | CD4                               | Mouse            | Rat             | IgG2a     | RM4-5       | BioLegend |           100533 | AF647       | AB_493372 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+| P06332                     | Primary Antibody | CD4                               | Mouse            | Rat             | IgG2a     | RM4-5       | BioLegend |           100533 | AF647       | AB_493372 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Spleen          | Healthy        | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:50.
+
+| Mouse Brain Tumor Hochest (Blue) mCherry (green, Novus #NBP2-25158 ) CD4 (Magenta, Biolegend #100533) |
+|:-------:|
+| ![](Mouse_Tumor_Brain_Hochest_Blue_mCherry_green_Novus_NBP2_25158_CD4_Magenta_Biolegend_100533.jpg) |
+
+
+| Mouse Spleen Hochest (Blue) CD4 (Magenta Biolegend #100533) |
+|:-------:|
+| ![](Mouse_Spleen_Hochest_Blue_CD4_Magenta_Biolegend_100533.jpg) |
diff --git a/...g_material/CD4_AF647/Mouse_Spleen_Hochest_Blue_CD4_Magenta_Biolegend_100533.jpg b/...g_material/CD4_AF647/Mouse_Spleen_Hochest_Blue_CD4_Magenta_Biolegend_100533.jpg
diff --git a/...in_Hochest_Blue_mCherry_green_Novus_NBP2_25158_CD4_Magenta_Biolegend_100533.jpg b/...in_Hochest_Blue_mCherry_green_Novus_NBP2_25158_CD4_Magenta_Biolegend_100533.jpg
diff --git a/docs/supporting_material/CXCL12_NA/0000-0002-6944-6997.md b/docs/supporting_material/CXCL12_NA/0000-0002-6944-6997.md
@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   | Clonality   | Vendor   | Catalog Number   | Conjugate   | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:---------|:-----------------|:------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P63158                     | Primary Antibody | CXCL12                            | Mouse            | Rabbit          | IgG       | polyclonal  | Abcam    | AB25117          | NA          | AB_2088164 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:100.
+
+| Mouse Brain Tumor Hochest (Blue) CXCL12 (Green Abcam #AB25117) mCherry (Magenta, Novus #NBP2-25158) |
+|:-------:|
+| ![](Mouse_Tumor_Brain_Hochest_Blue_CXCL12_Green_Abcam_AB25117_mCherry_Magenta_Novus_NBP2_25158.jpg) |
diff --git a/...in_Hochest_Blue_CXCL12_Green_Abcam_AB25117_mCherry_Magenta_Novus_NBP2_25158.jpg b/...in_Hochest_Blue_CXCL12_Green_Abcam_AB25117_mCherry_Magenta_Novus_NBP2_25158.jpg
diff --git a/docs/supporting_material/CXCR4_NA/0000-0002-6944-6997.md b/docs/supporting_material/CXCR4_NA/0000-0002-6944-6997.md
@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   | Clonality   | Vendor            | Catalog Number   | Conjugate   | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------------|:-----------------|:------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P70658                     | Primary Antibody | CXCR4                             | Mouse            | Rabbit          | IgG       | polyclonal  | Novus Biologicals | NB-100 74396     | NA          | AB_1048484 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:200.
+
+| Mouse Brain Tumor Hochest (Blue) CXCR4 (Green Novus # NB-100 74396) |
+|:-------:|
+| ![](Mouse_Brain_Tumor_Hochest_Blue_CXCR4_Green_Novus_NB_100_74396.jpg) |
diff --git a/...rial/CXCR4_NA/Mouse_Brain_Tumor_Hochest_Blue_CXCR4_Green_Novus_NB_100_74396.jpg b/...rial/CXCR4_NA/Mouse_Brain_Tumor_Hochest_Blue_CXCR4_Green_Novus_NB_100_74396.jpg
diff --git a/docs/supporting_material/CXCR7_DyLight_488/0000-0002-6944-6997.md b/docs/supporting_material/CXCR7_DyLight_488/0000-0002-6944-6997.md
@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   | Clonality   | Vendor            | Catalog Number   | Conjugate   | RRID   | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------------|:-----------------|:------------|:-------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P56485                     | Primary Antibody | CXCR7                             | Mouse            | Rabbit          | IgG       | polyclonal  | Novus Biologicals | NBP2-24779G      | DyLight 488 | NA     | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:100.
+
+| Mouse Brain Tumor Hochest (Blue) CXCR7 (Green Novus #NBP2-24779G) |
+|:-------:|
+| ![](Mouse_Brain_Tumor_Hochest_Blue_CXCR7_Green_Novus_NBP2_24779G.jpg) |
diff --git a/...R7_DyLight_488/Mouse_Brain_Tumor_Hochest_Blue_CXCR7_Green_Novus_NBP2_24779G.jpg b/...R7_DyLight_488/Mouse_Brain_Tumor_Hochest_Blue_CXCR7_Green_Novus_NBP2_24779G.jpg
diff --git a/docs/supporting_material/GFAP_eF570/0000-0002-6944-6997.md b/docs/supporting_material/GFAP_eF570/0000-0002-6944-6997.md
@@ -0,0 +1,22 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   | Clonality   | Vendor                   | Catalog Number   | Conjugate   | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State   | Detergent          | Antigen Retrieval Conditions   | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:-------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P03995                     | Primary Antibody | GFAP                              | Mouse            | Mouse           | IgG1      | GA5         | Thermo Fisher Scientific | 41-9892-82       | eF570       | AB_2573656 | Stock          | Multiplexed 2D Imaging | 4% PFA Fixed Frozen   | Brain           | Tumor          | 0.3%  Triton-X-100 | NA                             | NA                            | Yes         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | NA         | [0000-0002-6944-6997](https://orcid.org/0000-0002-6944-6997) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Dilution 1:50.
+
+| Mouse Brain Tumor Hochest (Cyan) GFAP (Orange Thermo #41-9892-82) |
+|:-------:|
+| ![](Mouse_Brain_Tumor_Hochest_cyan_GFAP_Orange_Thermo_41_9892_82.jpg) |
diff --git a/...ial/GFAP_eF570/Mouse_Brain_Tumor_Hochest_cyan_GFAP_Orange_Thermo_41_9892_82.jpg b/...ial/GFAP_eF570/Mouse_Brain_Tumor_Hochest_cyan_GFAP_Orange_Thermo_41_9892_82.jpg