MTI-R01_0092/README.md

# Marmoset Tracer-Injection [R01_0092]

Authors: Akiya Watakabe<sup>1</sup>*, Henrik Skibbe<sup>2</sup>

1. Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science
2. Brain Image Analysis Unit, RIKEN Center for Brain Science

*corresponding authors: Akiya Watakabe (akiya.watakabe@riken.jp)


## DATASET DESCRIPTION
    
This dataset contains **TissueCyte** images produced during **tracer injection** experiment on Marmoset **R01_0092**

* Microscopy images and annotations: Akiya Watakabe.
* Image post-processing: Henrik Skibbe.


For more details see https://dataportal.brainminds.jp/marmoset-tracer-injection


## EXPERIMENT METADATA
|||
|----|-----|
|Brain/MINDS ID|R01_0092|
|Group|Yamamori|
|Lab identifier|TT64|
|Region of injection|A24a|
|Side of injection|left|
|Summary|A24a injection ("mPFC").  Leak into Cd.  No label in A24b.|
|Known issues|Injection into narrow A24a.  No leak into above-lying A24b.  But small leak into the striatum (labeling of caudate cells lead to unusual labeling of striate-to SN pathway.)  IG (indusium griseum) may be strogly labeled which may innervate septum.  |
|Age|2.4|
|Sex|M|
|Body weight (g)|305|
|Date of birth|20160211|
|Injection date|20180703|
|Survival period (day)|27|
|&#x00A0;Tracer **1** |(thy1-tTA 1/TRE-clover 1/TRE-Vamp2mPFC 0.25)x10e12 vg/ml|
|&#x00A0;Direction|anterograde|
|&#x00A0;Method|0.2ul x 1 (@ 4.3 mm) 5min |
|&#x00A0;Tracer **2** |AAV2retro-EF1-cre: 1.5x10e12 vg/ml|
|&#x00A0;Injection Site|Coinjection with tracer 1|
|&#x00A0;Direction|retro|
|&#x00A0;Tracer **3** |10 % BDA|
|&#x00A0;Injection Site|contra-injection|
|&#x00A0;Direction|antero|
|&#x00A0;Method|0.5µl/5min x1|


## CONTENT

| File name | Description |
| ---- | ---- |
|[`NN_tracer`](NN_tracer)/||
|[`c2_50mu`](c2_50mu)/||
|[`labels`](labels)/||
|[`c1_50mu`](c1_50mu)/||
|[`c3_50mu`](c3_50mu)/||
|[`Backlit_slices`](Backlit_slices)/||
|[`Nissl_slices`](Nissl_slices)/||

**Note:** Color lookup table used in [atlas region labels slices](labels) can be found [here](https://cau-gin.brainminds.riken.jp/brainminds/BMA-2017/src/master/bma-1-clut.ctbl).
initial release 2021-12-27 00:00:00 +09:00			`# Marmoset Tracer-Injection [R01_0092]`

			`Authors: Akiya Watakabe<sup>1</sup>*, Henrik Skibbe<sup>2</sup>`

			`1. Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science`
			`2. Brain Image Analysis Unit, RIKEN Center for Brain Science`

			`*corresponding authors: Akiya Watakabe (akiya.watakabe@riken.jp)`


			`## DATASET DESCRIPTION`

			`This dataset contains TissueCyte images produced during tracer injection experiment on Marmoset R01_0092`

			`* Microscopy images and annotations: Akiya Watakabe.`
			`* Image post-processing: Henrik Skibbe.`


			`For more details see https://dataportal.brainminds.jp/marmoset-tracer-injection`


			`## EXPERIMENT METADATA`
			`\|\|\|`
			`\|----\|-----\|`
			`\|Brain/MINDS ID\|R01_0092\|`
			`\|Group\|Yamamori\|`
			`\|Lab identifier\|TT64\|`
			`\|Region of injection\|A24a\|`
			`\|Side of injection\|left\|`
			`\|Summary\|A24a injection ("mPFC"). Leak into Cd. No label in A24b.\|`
			`\|Known issues\|Injection into narrow A24a. No leak into above-lying A24b. But small leak into the striatum (labeling of caudate cells lead to unusual labeling of striate-to SN pathway.) IG (indusium griseum) may be strogly labeled which may innervate septum. \|`
			`\|Age\|2.4\|`
			`\|Sex\|M\|`
			`\|Body weight (g)\|305\|`
			`\|Date of birth\|20160211\|`
			`\|Injection date\|20180703\|`
			`\|Survival period (day)\|27\|`
			`\| Tracer 1 \|(thy1-tTA 1/TRE-clover 1/TRE-Vamp2mPFC 0.25)x10e12 vg/ml\|`
			`\| Direction\|anterograde\|`
			`\| Method\|0.2ul x 1 (@ 4.3 mm) 5min \|`
			`\| Tracer 2 \|AAV2retro-EF1-cre: 1.5x10e12 vg/ml\|`
			`\| Injection Site\|Coinjection with tracer 1\|`
			`\| Direction\|retro\|`
			`\| Tracer 3 \|10 % BDA\|`
			`\| Injection Site\|contra-injection\|`
			`\| Direction\|antero\|`
			`\| Method\|0.5µl/5min x1\|`


			`## CONTENT`

			`\| File name \| Description \|`
			`\| ---- \| ---- \|`
			\|[`NN_tracer`](NN_tracer)/\|\|
			\|[`c2_50mu`](c2_50mu)/\|\|
			\|[`labels`](labels)/\|\|
add c1, c3, backlit & nissl slices 2023-08-17 00:00:00 +09:00			\|[`c1_50mu`](c1_50mu)/\|\|
			\|[`c3_50mu`](c3_50mu)/\|\|
			\|[`Backlit_slices`](Backlit_slices)/\|\|
			\|[`Nissl_slices`](Nissl_slices)/\|\|
add link to region lookup table 2023-09-14 00:00:00 +09:00
			`Note: Color lookup table used in [atlas region labels slices](labels) can be found [here](https://cau-gin.brainminds.riken.jp/brainminds/BMA-2017/src/master/bma-1-clut.ctbl).`