在我們生物學(xué)的世界里，細(xì)胞類(lèi)型無(wú)論是交流還是位置都是在不斷的變化之中，當(dāng)形成一個(gè)成熟的組織之后，細(xì)胞類(lèi)型的位置才會(huì)相對(duì)固定，但真正意義上也是一種動(dòng)態(tài)平衡，當(dāng)發(fā)生疾病之后，免疫細(xì)胞的細(xì)胞類(lèi)型開(kāi)始發(fā)生變化，所以說(shuō)，研究細(xì)胞類(lèi)型之間的位置變化，也是一門(mén)很深的課題。

最近發(fā)表的一篇關(guān)于空間轉(zhuǎn)錄組的文章《Spatiotemporal analysis of human intestinal development at single-cell resolution》中，在研究腸道發(fā)育的過(guò)程中，提到了細(xì)胞類(lèi)型之間的距離分析。發(fā)育的過(guò)程中，肯定是有一些細(xì)胞類(lèi)型深入內(nèi)部，有的細(xì)胞類(lèi)型轉(zhuǎn)而向外，而有的細(xì)胞類(lèi)型在發(fā)育過(guò)程中隨著細(xì)胞類(lèi)型的移動(dòng)慢慢消失，所以有的時(shí)候我們對(duì)于組織結(jié)構(gòu)和發(fā)育的數(shù)據(jù)分析，更多需要這樣的時(shí)空分析，包括在研究腫瘤的過(guò)程中，細(xì)胞類(lèi)型之間的距離變化。
文章很長(zhǎng)，大家可以多看看，我們這里僅僅關(guān)注細(xì)胞類(lèi)型在空間上的距離判定，我們來(lái)梳理一下

Spatial transcriptomics spot distance-based analyses

1、在成年組織樣本載玻片中，標(biāo)記了肌肉黏膜，并始終用作參考點(diǎn)，對(duì)于胎兒組織樣品載玻片，在每個(gè)載玻片中標(biāo)記了完整橫截面的漿膜。（In adult tissue sample slides, muscularis mucosa was marked and used as a reference point throughout.），距離的判定需要一個(gè)參考，如果研究腫瘤，可以把腫瘤和正常細(xì)胞的邊界作為參考點(diǎn)。
2、In each slide, we then filtered out spots covering sections of tissue containing artifacts, including tissue folds. Spots covering the inner-most parts of the lumen were also filtered out, as these were found to contain mRNA signatures consistent with apoptotic epithelial cells, including very high mitochondrial content and low spot library complexity 這一步就是過(guò)濾，去除低質(zhì)量的spots，這里需要注意的是，凋亡標(biāo)志物，如果一個(gè)spot包含較高的某種細(xì)胞的凋亡標(biāo)志物，說(shuō)明該spot區(qū)域的細(xì)胞質(zhì)量很差，應(yīng)當(dāng)去除。
3、For each remaining spot, we then calculated Euclidean distance from the center pixel of the spot to the nearest marked up pixel。這個(gè)地方需要注意，歐氏距離的計(jì)算。Adult tissue sample slides were segmented prior to this to account for helical positioning of the tissue. Spots in the adult mucosa were assigned positive distance values to indicate distance toward the lumen, and spots in the submucosa were assigned negative distance values to indicate distance away from the muscularis mucosa.對(duì)于粘膜作為參考，將成年粘膜上的spot分配為正距離值以指示到內(nèi)腔的距離，將粘膜下層的spot分配為負(fù)距離值以指示與肌層粘膜的距離。Spots in fetal tissue slides were all assigned positive distance values to indicate distance toward the lumen。As the distance between spots between slides is uniform, this then provides a relative distance measure that is comparable between tissue sections.計(jì)算出來(lái)的距離就可以相對(duì)表示細(xì)胞類(lèi)型之間的距離。
Distance measures were then used to examine cell type score distributions relative to tissue depth in the intestine using density over distance plots.

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以圖片為例，腫瘤區(qū)域和正常區(qū)域的邊界作為參考點(diǎn)，我們來(lái)分析一下細(xì)胞類(lèi)型距離參考點(diǎn)的距離。當(dāng)然，最好用一個(gè)正常樣本的作為對(duì)照，距離的判斷對(duì)比更有意義。