Not any thalamus in the allen data

I cant find any mediodorsal or centromedian thalamus in the allen data???

Which data do you mean? It’s a structure in the CCF, and has gene expression and connectivity information. See for example this link from the connectivity atlas. 3d Viewer :: Allen Brain Atlas: Mouse Connectivity

Mediodorsal has abbreviation MD, and sits under the thalamus and medial thalamus in the hierachy (TH>MED>MD).

centromedian is under parafascicular nuclei complex magnocellular part (SPFm), under TH>SPF>SPFm.

Human brain!

This data.

Can find any mediodorsal thalamus.

If you downloaded one of those data sets from that page, you get a ZIP archive with several files. One of those files is Ontology.csv, which contains the list of structures and the hierarchy of structures. Mediodorsal thalamus is there as structure ids 4401 (for mediodorsal thalamus on the left side) and 4456 (for the right side).

You can also see which structures are in each column of the microarray data file (MicroarrayExpression.csv) by looking at the SampleAnnot.csv file. Each row of the SampleAnnot.csv file corresponds to a column of the MicroarrayExpression.csv file (in the same order).

If you look for structure IDs 4401 or 4456 in the SampleAnnot.csv file, you will see that they aren’t there. But if you look at their parent structures (seen in the parent_structure_id column in Ontology.csv), which have the IDs 4400 and 4455 (and are named “medial group of nuclei”), you can see several rows in SampleAnnot.csv that have that structure ID. So those would be the entries that contain data from mediodorsal thalamus.

The grouping of thalamus nuclei is described in the ontology documentation - quoting from that:

The ontology and nomenclature of the thalamus is based on The Thalamus (Jones, 2007), the premier work on the thalamus, as well as on personal communication with Edward G. Jones, who kindly supplied his ontology and nomenclature. This ontology and nomenclature extends to the epithalamus, as well as to those structures included in the ventral thalamus division, such as the zona incerta and the reticular nucleus of the thalamus. For tissue sampling purposes, the thalamus is sampled at a gross level, combining nuclei in a manner consistent with Jones’ subdivisions. Groupings for sampling from the dorsal thalamus, therefore, include anterior nuclei, medial nuclei, lateral nuclei (ventral and dorsal portions), posterior nuclei, caudal intralaminar nuclei, rostral intralaminar nuclei, the lateral geniculate nucleus, and the medial geniculate complex. From the ventral thalamus, the reticular nucleus and the zona incerta are sampled, the latter containing the Fields of Forel when present.

Wait I will look.

Couldnt find

This is from the Ontology.csv file from the ZIP file associated with donor H0351.2001:

Mine looks different

It looks like you’re having more issues with importing CSV files here. It’s splitting on spaces instead of on commas. I don’t know if that’s related to why you’re seeing different entries on different rows (for example, the solitary nucleus shows up starting around lines 1372 in my files), though.

You could try a few things:

  1. Try to import the file such that commas are treated as delimiters (so the columns are filled correctly)
  2. Confirm that you got this file from one of the donor ZIP files on the download page
  3. Check the top and bottom of the file to check that it isn’t truncated. The top should contain entries like:
id acronym name parent_structure_id hemisphere graph_order structure_id_path color_hex_triplet
4005 Br brain 0 /4005/ A0A0A0
4006 GM gray matter 4005 1 /4005/4006/ 787878
4007 Tel telencephalon 4006 2 /4005/4006/4007/ D988A3
4008 Cx cerebral cortex 4007 3 /4005/4006/4007/4008/ EDA65F
4009 FL frontal lobe 4008 4 /4005/4006/4007/4008/4009/ E8CD59

And the bottom should contain entries like:

id acronym name parent_structure_id hemisphere graph_order structure_id_path color_hex_triplet
9708 CPLV choroid plexus of the lateral ventricle 9419 1833 /4005/9352/9418/9419/9708/ 872601
9420 3V third ventricle 9418 1834 /4005/9352/9418/9420/ 231F20
9709 CP3V choroid plexus of the third ventricle 9420 1835 /4005/9352/9418/9420/9709/ 872601
9421 4V fourth ventricle 9418 1836 /4005/9352/9418/9421/ 231F20
9710 CP4V choroid plexus of the fourth ventricle 9421 1837 /4005/9352/9418/9421/9710/ 872601
9422 CC central canal 9418 1838 /4005/9352/9418/9422/ 231F20

The ontology file should have 1840 lines in it.

Wait a minute

Wow now it works! Horray!

Great - glad to hear it!

This work cant be done on a laptop correct?

I’m not sure exactly which parts of the analysis you’re referring to, but I would think most modern laptops would be able to handle most things you could do with these microarray data.

Mine cant. It stopsworking.