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GENSAT Retina Project Tutorial
Browse GENSAT Retina Project in NIF
For more information, visit GENSAT Retina Project Homepage or the NeuroLex entry for GENSAT Retina Project
GENSAT Retina Project is a database of confocal stacks, which can be freely downloaded and viewed in either ImageJ or the LSM Image Browser from Zeiss.
NIF presents the metadata for each image and a link to the appropriate page where images can be downloaded.
Terms such as retina connectivity and individual gene names will bring back this results set.
Below we search for gene:Rac3, one of the GTP-binding proteins in charge of regulating numerous cellular processes.
Data from this source can be found under Data Type > Images.
Note, the gene, expression level distribution and cell class are all represented along with a column for stratification.
The source (GENSAT Retina Project) represents stratification as a series of 0’s and 1’s. These numbers represent the possible connectivity stratification in the 11 layers of the retina starting with the Outer Plexiform Layer all the way to Inner Plexiform Layer 10. 1 means that connectivity is possible and 0 means that axons are not found in that layer.
The first position in the binary string corresponds to the OPL, and the last 10 to the ten IPL strata. Thus, the 11 digit string indicates the position where GFP positive neuronal processes have been seen.
For example:
The string 10000100011 would indicate the labeling in the OPL (1 - Position of the string) and in the IPL in stratum 5,9 and 10.
The string 00010000000 would indicate that we only see labeling in the IPL in stratum 4.
The string 11111111111 would indicate that we say a labeling all over the strata.
The string 00000000000 would indicate that we cannot find GFP positive neuronal processes in neither strata.
This binary string helps to predict possible connectivity between different cell types expressed in different mouse lines.
The NIF has translated these values to their corresponding layers.
Clicking on the image leads the user to the Retina Project at GENSAT:
Clicking on the confocal_503.lsm link allows users to download the data.
Note, both the Zeiss LSM Image Browser and ImageJ can be downloaded from links on this page.
For more information, please visit the Retina Project.
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